Due to IRS changes, credit card payments are not included in the 1099-MISC or 1099-NEC totals. Accounts Payable is working as designed.

As of version 9.8, the ability to enter credit card payments was added to Accounts Payable. The distribution on credit card payments entered using Tasks, Record Payments by Credit Card defaults to 1099 Exempt. The amounts will not be included when generating Forms 1099-MISC, 1099-NEC, or the 1099 Amount Paid Reconciliation reports attached to How do I verify my 1099 amount paid for a vendor in Accounts Payable?

In 2011 the IRS made changes to the 1099-MISC so that payments made with credit cards or certain other types of payments are now to be reported on Form 1099-K by the payment settlement entity. For more information, please refer to Instructions for Forms 1099-MISC and 1099-NEC and Instructions for Form 1099-K.