So this was a factory-installed bed liner? A factory liner shouldn't rattle at this point. I'd either get it fixed under warranty or see if they will pull it and credit you. They may not be willing to pull it and credit you as this was a factory install, not a dealer install. They should fix the rattle under warranty.
However, keep in mind that drop-in liners are subject to rattling. They can be padded and sealed in place but they are a big plastic tray dropped into the bed and are prone to coming loose. This is one of the big benefits of a spray-in liner.
