This is typical Gamestop policy. When they sell a brand new game, they make a few bucks. When they sell a used game for $54.99 that they bought from someone for $10, they make a lot more. That is why they push and push you to buy used games as opposed to a new games. I have no doubt the previous and next person to ask for Skyrim was told the same thing you were.

A Easter miracle in Tucson Gamestop

I decided to treat myself to a copy of Skyrim for my PS3, so off I went to my local Gamestop at Tucson Place. Once inside I asked the male assistant if they had a copy of Skyrim, he replied "only used" he told me it would cost $54.99, I said OK. It came in a generic box with no docs, just the disk, I asked if he had one with the original box, he said no. At this point I decided to go somewhere else for my game and thanked him. And then a miracle, the female assistant handed him a new sealed copy of Skyrim, out of thin air.
He scanned the game and I proceeded to pay with my card, and behold, the new sealed copy of Skyrim was only $49.99.
Now I must ask myself, after being lied to, and nearly cheated out of money, do I want to shop at Gamestop again? I very much doubt that.
This complaint was removed from Gamestop's forum

Oh please. Get over it.