First check the Expense Account it's being applied to. Maybe on some early entry it was incorrectly applied back into the Checking Account and QBs remembered that entry. It should look something like this:
Payee = (Bank's Name)
Payment Amt = (the fee amount)
Account = Bank Service Fees (or some other "Fee" Expense Acct - whatever you want)
The other option might be that the bank is charging you the fee, but you're a good enough customer that they are then giving you a credit. So are you sure they really are not two separate transactions? One taking the Fee out and then a second one the redeposit putting the money back in.