I had a store try the old "bait & switch" on me like that once. It's one of those stores that puts the empty boxes on the shelf which I understand, especially since they are all used titles (for the most part). I found a copy of Super Ghouls & Ghosts for the SNES. I was like, oh cool. Took it up to the counter, they rang me up and instead of putting the box in the bag with the cart, they set it on the shelf behind them. I said "Hey, box too." The answer I got back was "these are just for display." I told the clerk they needed to advertise that cartridge games are cart only, unlike PS1, PS2, Xbox, Gamecube, etc. which they give you the whole shebang. I said I wanted my money back and was told store credit only. I tried to reason with the hipster in the skinny jeans to no avail. Finally, I said "Look dude. You either give me my F*cking money back, or I'm going to kick your F*cking teeth in and throw your scrawny ass down the escalator!" I guess he understood the message as he got my money back from the register for me.
Now, I don't condone violence, especially over a video game. But this was a bullsh!t move by a shady company. And to make matters worse, I believe their online site sells games including everything in the picture. I had every reason to be pissed and wasn't leaving there with a half-ass, crusty cartridge and no box or manual. The place is called Slackers CD's & Games and they are located in St. Louis at the South County Mall. This was a few years ago, not sure if their policies have changed, etc. But I do know that the experience I had their jaded me to buying from them and the fact that all of their games are priced 50-100% higher than the larger used game store called V-Stock on the other side of the mall doesn't help their cause.
For the OP, that sucks man. Mom & Pop shops like them depend on customer loyalty and word of mouth to survive. Get a bad rep, you go under. Seems like they don't understand that.