Having a chain of ownership list would be a great help with this. Track and report which company owned the item back to it's manufacture and who 'owned' the IP of the run. Even more ideally also the production time, etc.
Good news, there is! It's called a database. When an item comes in, tag it with a unique barcode and add a row to the database saying "Item X came from company Y in shipment Z" and then sue/penalize/whatever company Y when it's counterfeit.
This assumes it is really that simple. You are adding a manual, human process. Humans make mistakes. Humans can intentionally make mistakes. Barcodes fall off, get defaced, etc. Those barcodes, hardware and software require money and up-keep. The humans receiving the products also can make mistakes and return the "wrong" item that happens to look the same (this is a source of counterfeits, even at Walmart/Target). And then we get into the shipment chain. Counterfeit swaps happen during the transit of packages to the warehouse and to the receiver's home. This is a really, really hard problem. And to be able to do it in a way that doesn't substantially raise the prices of the products only complicates that more.