Vendor Fees?

The companies I have worked for have always been on the receiving end of fees from our customers for doing something incorrectly (wrong pallets, late delivery, ect), but I have never had the opportunity to take a deduction not directly related to the product sold. In the example of the wrong pallets being used, we used the wrong pallets and the customer is now short-paying an invoice. Is the deduction taken by the customer being realized as revenue or as discount on the goods sold? Thank you.