QB Issue Resolution:

That means you should delete the Bill Payment check pending to print, and you select the Discount and apply it; THEN you pay it. You will see the discount taken in the shaded column on the right and the unshaded column in the Far right is the Net to Pay by check.

Resolution for Issue 'How to apply Vendor Bill discount' available: Yes (Solved).
Source: Intuit Community forum.

How to apply Vendor Bill discount: 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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