In most cases, it are computer systems that add those fees and whatever. They don't have an army of people going manually over every record.
In the software, rules are set up.
When I was a Lions Club treasurer, I received every month a bill for 1 cent. Apparantly, during a previous payment, the exchange rate had made that there was 1 cent left to pay. I was not going to pay just that 1 cent, but waited until a new real invoice arrived, because the international payment costs are high.
The computer at the Lions Club head quarters didn't realize it was just 1 cent; Computers don't think. They follow the logic that has been programmed into them. That's why every so many time, it sent me an invoice.
When you call, they can probably change things for you, but if it's just teh computer to decide, yes, you'll be charged with whatever fee.