Those multiple barcodes also confuse the crap out of self-check-out stations. Once it picks up on the wrong one, it throws a fault that the attendant has to come back out of, so you can't just back out scan the right one.
What baffles me is that the store/software can't build a dictionary of "known misdirection" barcodes, like "this is the shipping carton not the product itself, fault and tell the user to rescan, but don't just lock up" when they're seen.
Scanners in distribution centers contain a barcode hierarchy that filter out unused barcode types. For example, after something has been picked, a UPS label might be applied to it. Subsequent scanners will be programmed to only read either the internal routing label or the UPS label (or both and let the software handle it).
The scanners in supermarkets are made by the same companies and I would assume run on the same software. However, it might be more difficult to ensure a specific type of barcode is used on 100% of products in the store. So if you see the scanner picking up the wrong barcode at the check-out aisle, it is most likely either the scanner is not programmed correctly, or the scanned barcode is the same type as a valid barcode used somewhere else in the building.
As far as handling faults, that would probably be done on the POS system, not the scanner itself. The scanner software is perfectly capable of handling errors in different ways (for example, sending a specific code to indicate two different non-matching barcodes were read in the same pass), but from a functional standpoint, the scanner is 'dumb'.
What baffles me is that the store/software can't build a dictionary of "known misdirection" barcodes, like "this is the shipping carton not the product itself, fault and tell the user to rescan, but don't just lock up" when they're seen.