It might be different at FYE, but this happened to me at Gamespot just this weekend. I bought Metal Gear Acid2 used, but when I got home I noticed that it was actually Metal Gear Acid in the case. I came back the next day, explained the problem, and they realized it was their mistake and switched it out right away.

As long as you explain it to them reasonably, they shouldn't have a problem, unless they don't have the disk you need.