Courts martial were either regimental, field, or general. Only a general court martial could prescribe death.
Many of the men in the 91st who were court martialed were charged with absence without leave or desertion. The standard punishment was to lose pay and allowances for the time absent, and to be required to make up the missed time.
A few cases were more interesting. For example, Captain Alpheus Bowman and his first lieutenant Morris Kayser hated each other. After various provocations, Bowman called Kayser a "god-damned son of a bitch", and began punching him. He was found guilty of conduct unbecoming an officer, and dismissed from the army. However, the court martial had recommended leniency, and three months later, he was reinstated. When he returned to the regiment, Kayser went absent without leave. Kayser returned, and was assigned to a different company. Then, while the adjutant was under arrest, he was acting adjutant. When the adjutant was eventually released, he ordered Kayser to return to duty in Bowman's company, and Kayser refused. Later, when Kayser returned from unauthorized medical treatment in Washington, Sinex seems to have decided to throw the book at Kayser, charging him with two instances of absence without leave, and with disobeying the order to report to Bowman. Kayser was found guilty of absence without leave and of disobeying the order, but he was only fined two months pay and allowances! The reviewing authority found this penalty completely inadequate, but nevertheless affirmed it.
In a later case, Captain Joseph Gilbert was tried for disobeying an order and exhibiting contempt and disrespect towards his commanding officer. While the regiment was on parade for review, Lieutenant Colonel Sellers returned from a court martial, and ordered him to take command of company F. He asked whether he should take command of his own company, and when Sellers repeated his order, Gilbert said disrespectfully that "there was some God damned funny things [or work] going on here". His cross-examination of Sellers was inept, but the court determined that he did not have time to obey the order before Sellers placed him under arrest, and found him not guilty of disobeying orders, but guilty of disrepectful behavior. Two months after the trial, the court had not yet reported a sentence. Gilbert had attempted to resign, but Sellers refused to accept the resignation while they were waiting for the verdict. I don't yet have his file, but when the regiment mustered out, he mustered out as captain of his company.
The Articles of War include various laws about courts martial and offences, Article 38 of the Army Regulations prescribes more rules, and Article 27 prescribes rules for arrests.
For links to transcriptions, see archival records--court martial files