Yes - and not only during the Civil War. I have a great uncle who's given name was James but everyone called him Jack and he frequently signed legal papers as 'Jack'. One of my grandfathers had an argument with his brother and my grandfather changed the spelling of the last name which continues up to today. A lot often depended on what the clerk taking roll heard as well. If the clerk could not understand the name he might spell it phonetically or if he were lazy just put the person's surname down [as best he could spell it] and then just the soldiers initials for first amd middle names. It got better as time went on so that soldiers in the Spanish-American war usually had their surnames spelled correctly and in WWI they were usually using surname and First name; by WWII they were using all three names and if you didn't have a middle name. like my dad, they would issue you and initial to use.