Palletized sellable units - and how to handle Shipment ID labels

We sell items that come in manufacturer packaging that is suitable for sell as is. We cover the original barcode/EAN with the FNSKU label and then stack the goods - around 200 - on a single pallet. This is wrapped and the outside of the pallet contains the 4 pallet labels and the 2D Barcode Shipment IDs. We will send out 5 - 10 pallets like this at a time. 75% of the time they are received at the Fulfillment Centers without any defects. But. The other times we are told that there was a "Shipment Level Defect" and that the "Shipment ID Label" was missing. They claim all 200 sellable units in the order should have contained Shipment ID labels. But, wouldn't the 2D barcode negate the need? Could one even have a sellable unit labeled with both the FNSKU label and a Shipment ID Label?