This is happening because you did not choose "Payment" or "Credit Memo" as the document type when entering the transaction, which would have prompted you to enter the transaction as a negative.
Most likely, your transaction has gone in as a positive with no document type, causing the system to treat it as another invoice.
You cannot apply an invoice to an invoice.
- Solution:
- Reverse the payment transaction
- Redo the transaction with the correct document type
- enter the transaction amount as negative
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