it's possible the store didn't realize it was a boot, they may not have taken the time to reference it, and maybe don't see NEO games often enough to look into it.
I have a used book store here, really cool place, they had mvs metal slug x ($50) and Pulstar ($100) loose carts on the shelves forever. One Day after getting my cmvs, i decide to pick up the slug, got home, popped it in, and low and behold an amazingly poor version of Samurai Shodown 1 with some sweet graphical and sound glitches starts playing. The store has a 7 day return policy no problem, I asked my wife to return cuz I was busy with work, went back a week later and the pulstar wasn't there either.
This is a really cool store, and I don't think they would've knowingly sold that slug/shodown cart if they had known, I think they just didn't have any means of testing it when it was brought in for trade. Positive note, I just recently picked up a kof 2k with shockbox and great label from the same store, no boot, and works great.
Ibows, don't consider yourself boned, if you are not happy with it, you should return it, if it plays and looks ok, it might be ok to keep, but I think you could probably find a legit version from a member here for a little more than half the price you paid.
good luck buddy.