IMO, they need to just suck up the error and move on. It was not the client's fault in this case. It would be the same if a program had a bug and overpaid out all their affiliates and only notified the affiliates months later that they now owed the program $x money back.
However, I'm sure they are protected by their terms and offering to work it out instead of just taking it as one lump sum is nice of them to try at least.
This comes to mind:
