Here are a couple of examples re desertion:

February 1863 43rd Tennessee, CSA at Vicksburg

At three and one-half o’clock the Regiment was formed and two men,

John Keeling, Company B, and Wm Elkin, Company I, were marched

out in front, where their sentences were read and executed for

desertion. John Keilen was to wear a ball and chain for two months,

with the loss of two month’s wages, doing police duty all the while in

the Regiment. Elkins was tied to a post and given thirty-nine lashes on

his naked back. He then was branded on the left hip with the letter “D”.

This was all done by J. N. Stamper, Drum Major. Then Elkins was

drummed out of service to the tune of Yankee Doodle. This looked

pretty hard but he deserved all of it. The Regiment then returned to

camp expressing their dislike for such discharges. (Stamper)

These two men had previously been apprehended back in East Tennessee and where sent under guard to Vicksburg for Court Martial.

…..

Later

At twelve o’clock the remainder of the 43rd Regiment, together with the

3rd and 59th Regiments, went to see a soldier shot for desertion. I,

being with the Regiment, went to see him executed. At about two

o’clock the convict arrived in his shroud, riding on his coffin. The picture

of death was on his countenance. Upon his arrival a deadly silence

reigned all through the Division permitted [?]. Soon he was placed

against his post and [in] a minute he was shot dead, dead, dead. This

was a solemn occasion. He was a deserter from our Army and had

joined the enemy and had been taken prisoner. Three others were

shot the same day for similar charges, but not at this Division. Thus

we see that examples must be made for the good of others.

…..

However, it does not appear that your Nimrod deserted, he is recorded as having been paid June 30, 1863, subsequently he was reduced to the ranks from 3rd Corporal on August 20, 1863. Ten days later he was recorded as in jail, under arrest.

It thus appears he was present and must have been involved in some unlawful act. He could later have been court-martialed and dealt with in some manner, or lesser punished and returned to duty.