Well, there was that whole controversy when Deus Ex: Human Revolution came out. GameStop employees were ordered to remove and discard coupons that came with the game. I guess the-powers-that-be at GameStop didn't like the game coming with a coupon that promoted a competing digital distribution service, so they opted to just have their employees throw them out and not tell the consumer.
And speaking of employees opening up games that they then proceed to sell as new, there's the whole controversy about their employees opening up games and proceeding to sell them as new.
Also, did you know that GameStop employees are allowed to borrow new games to take home and play? Yeah, it's awesome, right? Employees in sales that will actually know a thing or two about a product before they sell it to people! That's a great business practice! Except for the part where the copy of the game that the employee took home to borrow is brought back to the store then sold to you, the consumer, as a brand new game at full price. Call me crazy, but generally speaking when someone takes a brand new item and uses it, that means that the brand new item is actually now a used item... and used items don't sell for full price. But have no fear, consumer! They just won't tell you whether or not the copy of the game you're paying full price for was played already, so there's still a pretty good chance that the game in your hands is new! Maybe!
Oh yeah... and that tiny little "screwing publishers and developers out of money thing" - that's an issue some people have, too... I guess.