Well first you were late, then they had to setoff the payment. So yes, you had the chance to pay and the fee accrued. Then they took the funds. It is common and likely your deposit agreement does allow for this. Loan contracts do as well, though not always a mortgage. But since it was in the deposit agreement, they were within their rights. They won't tell you in advance. If they did, many folks would opt to withdraw the money and the bank wouldn't have a payment to take. This can cause some customers to close and move their deposit account. But from the bankers perspective, it is easiest to say, don't be late, or if you must be, call and make arrangements. With pending arrangements setoff wouldn't be needed.