I want to ensure this unusual behavior is taken care of, @icutgrassllc.
I'd like to route this concern to the best support group available to get this addressed right away.
Since your customers receive notice that they made an overpayment on the amount of the processing fee, I recommend contacting our Merchant Services Team. This way, they can check on this matter further and provide some assistance on resolving this. They can also create an investigation ticket on this unusual behavior if other users are experiencing the same. To reach our live chat support agents, you can use this link.
I'm adding this article so you'll learn more about processing payment in QuickBooks Online: Take and process payments in QuickBooks Online.
Please touch base with me here for all of your QuickBooks needs, I'm always happy to help. Thanks for dropping by.