Hi, anthonytrave.
We're receiving reports that other users are getting this issue as well. We would like to inform you that this has already been escalated to our Engineering Team. While they do, I would advise you to get in touch with our QuickBooks Support.
This way our engineers can add your account information to the list of affected users and attach your case to the ongoing investigation. Any progress will be communicated via email.
The following article is a good reference: Frequently asked questions about Apple Pay and QuickBooks. It contains more information on how to process a reverse payment using the Apple Pay as well as handling chargeback.
Please extend your patience while we're working for the permanent fix. Don't hesitate to drop me a line if you have other questions about QuickBooks. Have a good one.