There was also the time back in 2006, when I had pre-ordered a copy of LEGO Star Wars II for GC. When I came into the store on release day to collect my copy, I was told that the store had only ordered PS2 copies of the game, they had enough, just all for the PS2. They offered me a PS2 copy or they could order a GC version from another store, which could take up to a week. Considering I had a PS2, with hindsight I probably should have just taken the PS2 copy, but at the time I wasn't exactly desperate and I was a stubborn 14 year old, so I decided to wait until my GC copy arrived about 5 days later.
That's not the online time they've cocked up concerning my pre-orders. Twice they've understocked a title and sold my pre-ordered copy (Timesplitters 3 and Super Mario 64 DS). At least on those occasions they gave me a gift card equal to the value of the game.