I think that's the difference between "new" and "refurbished". This would be more like the "open box" items you see slightly discounted at electronics places.

Anyways, I thought the common practice at these stores, for anti-theft purposes, was to remove the disks from all games before putting them out on the shelf. When you select a game, they replace the disk from behind the counter, shrink wrap it, and put an anti-tamper sticker on it. I buy games occasionally for my nieces and nephews and that's what they do every time. Maybe it's just the store I go to?