Regardless of how it was calculated (right or wrong), you must collect what the note says. The problem you have identified will have a tiny impact on the amortization of the loan--certainly not enough to necessitate a rewrite of the note. Reading the note, you will most likely find language calling for payments of the stated amount until all principal, interest, and other amounts due have been paid in full. Following that prescription, you will not overcharge the customer.
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...gone fishing.