Yes, they have the option, but

they may don't do it. An extra refunding process is indeed an extra work. So who is going to pay that part? A similar case is the I140/I485 concurrent filing. If the I140 is denied, there will be no refund for I485. And it is also improper for USCIS to charge for some services that they don't actually perform. Then why people don't think this is an overcharge?

The option that USCIS takes this case (with $100 over charge becasue of the mistake of the petitioner) is really the best scenario that I can think of. And if I were the petitioner, I definitely hope that USCIS will handle this case with the overcharge insteading of messing around with rejection/resubmission.

Well, I don't want to argue. So just take it for fun:)