Throughout time all armies have found it necessary to maintain some form of discipline and the Civil War was no exception to the rule.  When the armies of the north and south formed up and officers and enlisted men were learning their place and respective duties, there were three times the number of punishments administered for poor behavior as in the latter two years of the war.  This is in part due to several circumstances.  In the last years, the Confederate army was totally consumed with its survival and the Union army was pushing hard for a victory.  The rigors of the marches into position and then into battle, the months spent campaigning the hardships jointly endured by all from privates to generals and the unity towards a common goal brought the men together.  There were still discipline problems but only the gravest of crimes warranted attention.  As the war drug on, trivial offences were committed but they were often ignored.

Types Of Courts Martial.....For the most serious infractions, officers were usually subjected to a General courts martial and enlisted men were dealt with in Regimental or Garrison courts martial.  The General courts martial (photo at left) was convened by a general staff officer or a colonel.  The Regimental courts martial was a panel of three officers (up to a maximum of thirteen) headed by the regimental or corps commander's appointee.  The panel was made up of commissioned officers only excluding chaplains, surgeons, paymasters.  The Garrison courts martial included a panel headed by the garrison commander's appointee for charges against the soldiers within forts and camps.  The Drumhead was not really a formal courts martial and could be called by any commander for any reason while in the field; furthermore, legal formalities were usually disregarded.  The Drumhead type of courts martial led to a wide range of inequities as the officers used their own judgment and meted out what they perceived to be fair punishments.
  In all types of courts martials, a judge advocate was appointed to represent the government (same for Union or Confederate) whose job it was to prosecute.  The problem with the judge advocate was that he was also to represent and defend the accused and additionally had the right to prevent "any record from being made...which (might) influence...the witnesses whose testimony is yet to be delivered."  Men could be beat or bribed into making confessions and leading questions could be used to confuse the accused.  The cards were clearly stacked in favor of the army.
  The problem with courts martials was that the military justice system requires witnesses for prosecution and defense.  Witnesses often were killed or missing in action and the officers required to sit on the board were not always available. In addition to that problem, there were no specific guidelines for most minor to semi-serious offences as they were not covered by the military code.  Before any appropriate punishments could be administered, a courts martial board as specified in article 66 of the Customs of Service had to vote with a two to one majority in agreement that a punishable crime had been committed.  There were no pardons except from the commanding general or from Presidents Davis or Lincoln.  The accused could challenge a decision made by the court but the court did not have to consider the challenge to their decision if they didn't want to.  As you can see, the courts martial system of military justice is clearly contrary to the Constitution.
  Punishment for crimes or behaviorisms was not limited to the enlisted men and non-commissioned officers only; however, enlisted men suffered far greater punishments than did the officers.   For example, an enlisted man if found drunk was often sentenced to wear a ball and chain for a month while an officer committing the same offence more often than not was not punished at all.  Officers were subject to and frequently were tried for their offenses.  More often than not, the sentence administered to the officer was limited to the less severe punishments of fines, confinement to quarters or assignment to an undesirable command.  In cases of high disgrace, the offending officer was expected to resign.  The infantry, cavalry and artillery handled their discipline problems in much the same way but the Navies of both the North and South dealt with their discipline problems differently.  Aboard ship there was no place large enough to set up a punishment area and the lack of personnel prohibited most corporal punishments.  The Captain of the ship dispensed justice as he saw fit.  The punishments were usually in the form of fines, extra duty, time in the brig, confinement in single or double irons, confinement on bread and water, solitary confinement, or reduction in rank. 

There were literally hundreds of circumstances and behaviors during the Civil War that resulted in punishable offences committed by both officers and enlisted men.  Some men were guilty of serious crimes, some intentionally misbehaved to avoid the problems of camp life, while others were just in the wrong place at the wrong time.  General McClellan often complained about the leniency demonstrated by sentences handed down from the courts martial boards.  He felt that softer punishments encouraged the perpetration of crimes.  McClellan himself confirmed five death penalty sentences.  Approximately 500 soldiers (north and south combined) were executed for capital crimes.  The Union army's records show that they executed 267 men. This included 147 deserters, 67 murderers, 19 mutineers, 23 rapists and 11 others for various crimes.  Overall, the unit commanders held the record for the most severe punishments (not including the death penalty).  They were able to arbitrarily sentence men while in the field in a drumhead courts martial. 

Defying Orders........You may think at first that defying orders was a problem with the common soldier but in fact this problem manifested itself most often within the ranks of the officers.  Union Brigadier General Henry Washington was arrested on June 19, 1862 for disobeying Major General David Hunter's direct written order not to advance upon the Confederate Fort Johnson and Secessionville.  Washington was weary of being harassed by the Confederate artillery and attacked the fort even after his fellow officers advised against it and he had been ordered not to do it.  The assault was attempted on June 16, 1862 and within twenty-five minutes more than 500 Federal soldiers lay dead or wounded.   The General should have been convicted of a serious crime in the death of so many men but instead, after the intervention of the President, he was relieved of his command and his brigadier commission revoked.  Brigadier General Henry Washington was reassigned to engineering duties with the Army of the Potomac and remained there throughout the war.  In some cases, defying orders escalated into outright insubordination and sometimes violence.  The ninth article of war stated that any violence toward an officer could be punished by death.

Sleeping While On Duty........Guard duty for many reasons was the most dreaded part of a soldier's routine duties.  Hundreds of men fell asleep while trying to perform this job.  It was mentioned in many letters home like the one below.
 

"I saw my first example of "Army discipline" today - and don't like it one bit.  Tommy McKearnan fell asleep on guard duty last night.  After all, it had been a long day, what with the skirmish then the ride down to here.  Tommy was beat before his squad drew the guard.  He was caught by the sergeant of the guard early this morning, and placed under arrest.  They didn't even bother much with a trial - he was guilty anyway.  As punishment, they've stripped him down to his underwear, and are making him wear a barrel around camp with a sign on it "I Fell Asleep"  He'll probably be back on duty tomorrow.

In another regiment, they "bucked and gagged" a soldier for the same thing.  Talk about cruel - they gagged the poor guy, made him sit on the ground with his knees up, then tied his hands around his ankles.  To make sure he didn't get loose, they ran a stick between his arms and his knees.  Then, they left him like that for 8 hours!  Glad I'm in the 40th Ohio - we don't do that stuff.  But, you betcha I won't be falling asleep on guard duty to find out!"

Oddly enough, I found several examples like the one above where the soldier received what would be considered light punishment for sleeping on duty but the Regulations for the Army of the United States took quite a different view of this problem.  In the articles of war section it is written:
 

Art: 46.  Any sentinel who shall be found sleeping upon his post, or shall leave it before he shall be regularly relieved, shall suffer death, or such other punishment as shall be inflicted by the sentence of a court martial.

Apparently the last part of that article saved many a man's life.  The courts martial had the last word in the matter.

Slackers And Stragglers.......It was imperative that the army on the move kept together and in motion.  Some soldiers could not keep up the pace but others chose not to keep up.  Those who fell behind for lack of motivation were called stragglers.  Those soldiers could be punished by being bucked and gagged.  At the second Bull Run, Confederate Brigadier General Charles S. Winder was leading five volunteer regiments.  When thirty men intentionally fell behind on the while marching, he had them all bucked and gagged at once.  The punished men swore to kill Winder at their first opportunity but he fell mortally wounded and soon died in the next battle.
  There are always slackers in every facet of life.  In the military, most soldiers who avoided duty were punished by being made to walk around camp with a sign around their neck upon which slacker was painted or they were made to stand on a wooden barrel.  Confinement to the guardhouse for a slacker was just what he wanted so they were seldom given that punishment.

Alcohol Abuse.......One of the most common offences committed during the war was alcohol abuse.  The armies of both sides did their best to discourage drinking and always punished drunken soldiers but neither the Northern or Southern army made much headway in the elimination of alcoholic beverages.  In February 1862 Union General George McClellan said "No one evil agent so much obstructs this army... as the degrading vice of drunkenness.  It is the cause of by far the greater part of the disorders which are examined by courts martial.  It is impossible to estimate the benefits that would accrue to the service from...total abstinence from intoxicating liquors.  It would be worth 50,000 men to the armies of the United States."  In some camps the problem surrounding bootleg whiskey was to great to deal with and the commanders decided to just try to control it.  As early as the 1850's areas in camps were established, controlled and strictly supervised by NCOs where drinking was allowed.  The drinking of alcohol was addressed by article 45 in the Regulations for the Army of the United States:
 

Art. 45.  Any commissioned officer who shall be found drunk on his guard, party, or other duty, shall be cashiered.  Any non-commissioned officer or soldier so offending shall suffer such corporeal punishment as shall be inflicted by the sentence of a court-martial.

The soldiers obtained almost all of their alcoholic beverages from the camp's sutlers.  When alcohol was available for sale, the sutlers would have a special signal to let the men know.  The signal could be as simple as half of their tent fly folded back at an odd angle or a barrel turned sideways beside their wagon.  The army took a dim view of this but could do nothing more than making the offending sutler leave the camp and not allowing him to return.
 

Art. 29.  No sutler shall be permitted to sell any kind of liquors  .. (etc. and goes on to state)  ..  on the penalty of being dismissed from all future sutling.

Civilians would also try to sneak liquor into the camps and sell it to the soldiers.  If they were caught, the alcoholic beverages were destroyed and they were usually escorted out of camp.

Gambling........When large groups of men get together for extended periods of time several things are bound to happen.  First they will use a lot of profanity and posturing to achieve status, second they will fight, and lastly they will gamble (which usually led to more cussing and more fighting).  The War Between the States was no exception to the rule.  In 1864 gaming in Federal camps was so prevalent that the Army of the James was known as the "Army of the Games" among the men.  The same games were played then as are played now.  Val Giles, a Texas soldier wrote home "There is a strange, unaccountable fascination about gambling.  I have known men who never threw a card before the war began, or have bet a cent since it closed, to lose the last Confederate dollar they had, betting at a game they really knew nothing about".
  Gambling hasn't changed much in the last 140 years.  The most popular gamblers game came in the form of card playing.  "Throwing the papers" was something everyone could do.  If a soldier wanted to learn to play cards, he could always sit down to a game with some eager teachers.  Draw poker was the game of preference but if a man didn't care for poker, he could still "take a twist at the tiger" in the form of twenty-one, keno, euchre, and faro.
  Two popular dice games were "craps" and "sweet-cloth" (also known as "bird cage").  The crap game in camp was quite different than what we play today but the basic game is still the same.  Sweet-cloth was a game wherein three dice were tossed from a cup onto a flat surface.  The players bet on the various numbers that might appear on the three dice when rolled.  The man who had guessed the correct total beforehand won the pot.  Horse races, cock fights, boxing matches, even a friendly game of checkers; no game was immune from a friendly wager and if a soldier gambled away all his money he could still play by resorting to the use of "O.P.'s" also known as an "order on the paymaster".

Desertion........Men started leaving the ranks without permission as early as First Manassas but didn't reach its highest point until the Shenandoah Valley Campaign in December, 1862.  There were 180,000 Union men absent with or without leave.  General Hooker reported in 1863 that 85,000 officers and men had left the Army of the Potomac.  More than fifty percent of the Stonewall Brigade abandoned the ranks.  As the morale of the Union army fell, the desertion rate increased.  In the fall of 1863 as desertions increased so did executions.  A North Carolina lieutenant watched as a deserter was shot near Orange Court House, Virginia. in October 1863.
 

"The one that was shot today was not killed dead the first fire." he noted.  "Consequently he was shot twice.  You can not imagine how cruel it looks to see a man shot.  Twelve men shot at him at about ten steps;  Only one ball hit him in the side.  He fell over on his face, was examined by the surgeon. who pronounced him not dead.  Two men were then ordered out with loaded muskets who shot him dead.  It looks very barbarous to see men shot in that way but it is necessary to maintain the discipline of an army."

At its highest level, 280,000 Federals deserted.  It is estimated by some that one in seven Union soldiers deserted and in 1864 the Federal desertion average per month was 7,333 men.
  Although the Confederacy had as all armies throughout time have had a problem with soldiers deserting on any given day and even during battle itself desertion in the southern army was far less extensive than in the northern army.  Only about 104,000 Confederates, far less than half as many as the Union forces, deserted their comrades.  Estimates claim that one out of nine Confederate soldiers left without permission.  President Davis tried to curb the desertion rate by offering its soldiers a $100 bond in exchange for a promise not to leave.  The Civil War set the record for deserters.  The average rate for both armies at any given time was an incredible 11% of their total available strength. 
  The sentence for this cowardly act has been carried out in many different forms including flogging, imprisonment, a "D" branded on the deserter's face or death by firing squad.  Yes, it is true that the flogging and branding of deserters was an acceptable form of punishment as far back as the Whiskey Rebellion in 1794.  Although these punishments were common and imposed with shocking severity during that time period and both were authorized in 1861-1865 War Between the States, neither were used with regularity.  Usually deserters when recaptured were put to hard labor on government works or confined in a penitentiary to work out their unexpired term of service.  Strangely enough was the fact that in the Union army less than 10% of those convicted of desertion actually died at the hands of a firing squad and a quarter of those sentenced received commutation.  Executions for desertion in the South ran higher.
  Both the Union and Confederate army took the problem of desertion very seriously.  The death penalty was recommended by both armies for this crime.  The Regulations for the Army of the United States addressed the problem thusly:
 

Art. 20.  All officers and soldiers who have received pay, or have been duly enlisted in the service of the United States, and shall be convicted of having deserted the same, shall suffer death, or such other punishment as, by sentence of a court-martial, shall be inflicted.

The exception to this rule was an article passed on May 29, 1850 that read:
 

"No officer or soldier in the army of the United States shall be subject to the punishment of death, for desertion in time of peace."

As a last resort, Presidents Lincoln and Davis, issued impassioned pleas, proclamations, pardons and amnesties to the deserters but the tactic met with only limited success.

Minor Punishments For Minor Offences......There were many offences committed by the everyday soldier, most weren't worth the time and effort necessary to carry out the punishment but the armies of both sides had to maintain order.  If a man was caught committing petty theft, absent from or late to roll-call, rowdiness after taps, gambling, talking while in ranks, minor disrespect to a superior officer and other insignificant problems, the man was dealt with in a more humiliating form of punishment as opposed to a physical punishment.

References:
Library Of Congress
The Cry Is War by Taylor
War Letters by Andrew Carroll
U.S. Army Military History Institute
Southern Invincibility by Wiley Sword
Hard Tack And Coffee by John D. Billings
A Brotherhood Of Valor  by Jeffry D. Wert
Soldiers Blue and Gray by James Robertson
Customs Of Service For Officers Of The Army
Fighting Men Of The Civil War by William C. Davis
Regulations for the Army of the United States Revised 1861
Customs Of Service For Non-Commissioned Officers And Soldiers