I am not surprised by this, since it seems like every time I have gone there to buy something it is always the last copy. Conveniently, the last copy is the one they have on the shelf and it has been opened and put in an envelope behind the counter. It probably has also been taken home and played as Redeema has mentioned above. Last time I checked when something is opened before you buy it then it is considered used, but you have to pay full price for the last one at GameStop. Most stores give you some kind of discount on the floor model items, which is what I would consider these games that have their cases on the shelves for people to view.
Maybe all the Deus Ex: Human Revolution games with the OnLive code are really the "last copy" when people buy them and they happened to remove that insert, since it didn't fit in the plastic bag behind the counter.