This cannot happen if you use "Generate Creditor Payments", only if you use single Creditor payment transactions. If, instead, you build up a batch of single transactions to be processed and choose the same creditor twice, then two payments can be created for the same invoice.
To fix this :
1. Process a normal invoice creditor using a Suspense account property.
2. In the Transaction History, locate the new entry and choose Edit. Enter a "1" in the Invoice Paid By field, and save the transaction.
3. Process a negative amount invoice using the Suspense account property
4. Process a creditor payment against the negative invoice.
5. Reconcile the new reversed creditor payment against the duplicate payment.