"Brand new at Gamestop" is kind of a contradiction in terms in some places. GameStop is notorious for removing the factory shrink wrap from new games. All bets are off after that. I've never had a problem redeeming a code in a game that I purchased from Amazon. Unless the game was factory shrink-wrapped, and not heat shrink-wrapped, the code might have been used before even if the game was sold to you as new, especially at Gamestop.
I'm having the same problem, bought a brand new U3 goty and it says the pass is in use! Has your issue been resolved? If not what should I do? Buy another code? It's quite frusturating since I have already spent 40$ on the game.