Yeah... it sux. I had to deal with this crap on a daily basis when I worked there last year. It's unfortunate, but thing is... the company is required to draw in more revenue than it gives out (in the form of "ripping you, the consumer, off) . You'd actually be surprised to know that this is more or less the standard for most producers (the guys selling you stuff), particularly those that follow the "buy, sell, trade" paradigm.
I once sold them my Wind Waker, and walked out with a whopping 20 bucks. Yeah... Turns out that if you take a look at the receipt you can clearly see that many factors play into the amount of cash you'll get back. Said factors include, but are not limited to, date of purchase, the condition of the game at the time of return, and demand and popularity of the game, although only the former two factors can be seen on the receipt. My copy of WW was not only a month old, but it didn't have any scratches or pricks and I can assure you that it was in high demand at the time.
In any event... I am baffled as to the [hidden?] factors involved in your transaction, but it does seem quite unfair. All I can say is to follow Furie's advice if you ever plan on paying another visit to Gamestop; used games are entirely different animals...