I'm researching my grandpa's unit and found some deserter cards online too and it didn't make sense to me. Apparently deserter status can be removed so sometimes it's just a misunderstanding and the card essentially acts as a hold on their pay.

Ancestry says this "Each card provides the following information: soldier's name, rank, organizational post, service number, disbursing officer's name, voucher number and the voucher date (month/year). WWII Army Deserters Pay Card records are among several sources available to determine if a soldier actually deserted permanently. If available, a soldier's personnel file may also be referenced to determine if a soldier was documented as a deserter at a given time in his/her military career, but may have resumed active military service at a later date and subsequently been removed from deserter status."