QB Issue Resolution:

You must be using banking downloads for the CC, and the transaction downloaded

two options

1. delete the download transaction and use pay bills to pay the bill with the CC
OR
2. edit the entry in the CC and as the expense account use accounts payable, then use pay bills, select the bill and apply the credit that edit made

Resolution for Issue 'How to record a payment by a credit card on vendor’s bill in QB? If I go on Make payment, choose vendor, date and credit card, it duplicate ending balance on card.' available: Yes (Solved).
Source: Intuit Community forum.

How to record a payment by a credit card on vendor’s bill in QB? If I go on Make payment, choose vendor, date and credit card, it duplicate ending balance on card.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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