Admins have the ability to override most fees being charged to users. This can be done to provide a discount, to collect previously owed fees, etc.
On the check in/out page, there is an "override" box below or to the left of most fees being collected. For example, in the Check Out Area:
In this case, a $15 rental fee was changed to a $10 fee. To completely clear/remove the fee, simply set it to 0 (zero). You can override late fees and membership fees in a similar way. The summary area of the check out page will tell you (and record in the system) the total amount that was originally calculated to be due, and the total amount actually paid for this transaction.