If the circumstances are as you described, I agree with Randy 100%.
If, however, the third parties charged the bank and the BANK subsequently waived the fee (by eating it and not passing it on to the employee/borrower), you don't have an issue. Ideally, all the charges appear on the HUD-1 (if RESPA-applicable) as POC items.
_________________________
Opinions are Bartman's, not those of my employer. "A noble spirit embiggens the smallest man."