Game Informer spoke to a few stores, and found Best Buys expecting copies on February 6, and GameStops expecting them on February 8. We've checked in with Nintendo for more information on the supply issues.
In the meantime, there are no supply issues on the 3DS eShop, where Fire Emblem: Awakening launched this morning.
Update: A Nintendo spokesperson provided the following statement to Joystiq: "Nintendo makes every effort to make sure its games and systems are available at retail stores nationwide on launch day. Sometimes, because of the variables of shipping, different retailers receive their shipments on different days. Fire Emblem Awakening can be purchased right now from the Nintendo eShop for Nintendo 3DS."