We just found that our loan processors were charging fees for credit reports that were not actually the fees we pay our provider. In all cases the fees disclosed on individual loans was higher than we are charged. Should we give back the difference to our borrowers or how do we cure this violation?

That's likely how I would go about it. Is it possible that they were using an average charge that they didn't adjust when they re-evaluated the charge?

Unfortunately no, the average method was not even considered.