I would agree with that conclusion from Mark's post. You'll learn something by comparing your soldier's record with that of other men from the same company. I would also suggest that you find the regimental cards at the beginning of the records for the command in question. This will tell you exactly how many muster rolls and other rosters are being used to compile these records.

For instance, let's say your soldier's name appears on the muster for March-April 1862 as present, but it's not on the roll for July-August 1862. The regiment has no records for May-June of that year. It's easy to conclude that he was removed from roll during the last-named period. Based on these records, we won't be able to say exactly why.

Would you mind sharing the name and unit of the soldier you are reviewing?