First of all, I would like to say that I'm sorry you have had trouble with this.
Unfortunately, there's not really much you can do. There is no way that you can prove that the product was that way when you bought it, and there's no way Best Buy can prove that the item was returned incorrectly.
This happens a lot. When I first started working for Best Buy, I was given an iPod to put back on the shelf that had been a return; when I thought it felt kind of heavy, I opened it, and found two ceramic tiles in the box. Customer Service laziness has always been a problem. How much effort does it take to look in a box and look at the picture on the box and determine if they're the same thing? Just the other day I was given a camcorder to put back on the shelf that had been returned as new-in-box, even though it had an open-box sticker on it from another store, and had been returned with no battery, charger, or cables. Trust me, it's just as frustrating to employees as it is to customers.
But to play devil's advocate, we get A LOT of customer fraud like this. We have to call a manager now, every time a harddrive or graphics card is returned, so the manager can inspect it before we can return it. There's a huge problem with customers buying a new product, putting their old product in the box, and returning it, saying that the wrong product was in the box when they bought it. And we have no way to prove if the customer is lying or telling the truth.
What I would do is call 1-888-Best-Buy and talk to corporate about it. Corporate can get in touch with the district manager, who has much more sway than the store manager does.
I hope you get this worked out!