I've in-store pre-ordered stuff from GS/EB stores before (before and after the merge) and had this happen. Was I upset? Yes. Do I know if the store even got enough to cover the pre-orders? No clue, but I know this is often the case that they didn't even get enough to cover orders.

What I have done since then though has gotten me my special item ever time. I order it online. Either Amazon or GS online orders (if done before the game releases) that mention the special goodies when you order it will give them to you. Sometimes a game might be delayed a day or two in shipping out (seems to happen to amazon) but i'll be damned if I don't get my goodies using this method.