So the granola company, coaster company, etc. forgot to remove the old bar codes from the outermost box before packing it full of their own product and sending it out. One could tell them this, but there will probably always be more small companies making this mistake.
Probably what should happen is for Amazon to mark this item (the box of boxes) as requiring special handling when scanning on entry into the warehouse, verifying that it actually is a box of boxes (right weight, no other barcode, etc), and explaining why. And audit all the ones currently in the warehouse.
I have no idea how to convince Amazon to do this. Like the author, I'd give up and start buying my boxes elsewhere.