Answer:
I would not recommend that the bank require their registration based on single mistake, especially if it was an instance in which a single individual cashed more than one check at different times during the business day, or with different cashiers.
Instead, I suggest reminding the customer of its own policy and that they will have to register with as an MSB with FinCEN (and possibly the state) if they fail to follow that policy. Then you might consider reviewing the business's check deposits more frequently for a period of time.