My guess would be they pulled the mats at the original dealer to keep them clean. A lot of dealers will throw down the disposable paper mats and keep the OEM mats in the back seat. The dealer may have pulled them out and when your dealer grabbed the truck they didn't throw them back in.
If your truck has locking lug nuts check the glove box to see if you have a small white bag, it should contain the security key for the locking nuts and 4 normal lug nuts to replace the locking ones if you wanted.
Make sure you have the owner's manual it will be in a leather sort of portfolio. Beyond those two things I can't think of anything else that MAY be missing. Check to see if you have the tailgate kit, its a sealed baggy. Check all the seat pockets, center console, glove box, anything that opens up check.