In all honesty, they should have given you a good copy to begin with. Since you went through the trouble of going in and giving them money ahead of time. Seriously, if it was me I would be livid to the point of telling them to shove their shitty smashed copy.
Usually the copies have always been good, occasionally better than what I've gotten through Amazon (separate artbooks like the one for FE:A, for instance, were more dinged up from Amazon); this was the one of the first times I was disappointed in the condition of what they were giving me. I'm not the sort to make a fuss, though, but I will likely return the game after receiving another copy from Amazon.
The other time I've been disappointed by the condition of something they gave me was the steel case for Ni No Kuni, but apparently *all* of them had minor scratches and dents.