Create a Vendor Credit
Raise it against the bill that was wrong, with the receive as your evidence.
A vendor credit records money the supplier owes you back. Most of them start as a mismatch the receive caught.
Raise one
Open the bill and create a vendor credit from it
The lines carry across and the two documents stay linked.
Trim to what is actually being credited
The short quantity, the price difference, or the damaged units.
Say why, and attach the evidence
The purchase receive is the document that proves a shortfall. Photographs help for damage.
Save, and send it to the supplier
A credit they do not know about is a credit they will not honour.