I have the same issue.  Let me be clear, as the Quickbooks team in this chat don't seem to understand.

Until about 1 month ago, I would issue an invoice to a customer (Quickbooks online).  I have a box checked so they would get charged a 3% convenience fee for a credit card.  Quickbooks automatically issued a second invoice for the convenience fees and applied the 3% to that.  It worked fine.  Now, it stopped automatically generating the second invoice and just tells me I have a 3% over payment?  Do I now have to manually create a 3% invoice when somebody pays me?  That's not convenient for me.  Why did QB change this, and how do we get that feature back?