Purchase Order Discount / AP Question

To start, I am not a financial person, so if this question sounds very basic and ignorant, that would be me!

We have a situation where a purchase order was written with three line items. The PO indicated the price for each of the items. When the invoice arrived, The supplier applied a discount we were not expecting, unique for each line and we are trying to figure out what is the best approach to balance the two. Should we make the adjustments on the AP entry or go back and update the PO?

Thanks,
Tim