You need to contact the bank/lender that issued the Form 1099-MISC and get an explanation for why it was issued. In the meantime, you should wait for an explanation (or correction) before deciding how to report the 1099-MISC. The IRS will be looking for this on your tax return, so not reporting it is a risky option.
"Waiving a fee" does not qualify as income to you; it would just be a reduction in whatever cost the fee was for.
