Be careful, if your system considers the late charge (the one that the bank did not notify the customer that it had assessed) in calculating the payment, and the bank does not consider the payments received are "in full", it may have a pyramiding issue, and at least a possible violation of state law and/or UDPAA,
I would consider these best to be absorbed by the bank and potentially a claim to the vendor under their reps and warranties provision.
Integrity. With it, nothing else matters. Without it, nothing else matters.