When you do the 1040X, it calculates the balance due taking previous payments, previous refunds and whatever is left (in this particular case) the balance owed.  They received 3600 in Recovery Rebate and the program doesn't calculate that as a previous payment so it adds the 3600 to the balance due.  I can enter it manually as a refundable credit, then the balance owed is correct but shouldn't have to do that.