They could require the vendors attach the stickers to uniquely determine the shipment. Upon receipt, just scan to ensure the barcodes match/aren't duplicates. They already require vendors using Fullfillment by Amazon to have their shipment contain a shipping summary. Adding per item barcodes wouldn't be a huge change (and Amazon itself wouldn't bear the cost).

You're right. The items have to be scanned for inventory management anyway when they arrive and are put in the bins at Amazon. Might as well just scan a second bar code to note where it came from. Or do it as a combined QR code. Lots of room for extra data in there.