Oh yeah, I've had this problem multiple times in the last year.
One time was for a CIB copy of Otomedius Excellent which he couldn't find the disc, twice for Dragon's Lair Trilogy because one time the case went missing( but found later and sold to someone else even though I had a pickup at store request), and the other time because someone stole the case. It also happened on a copy of Dokapon Kingdom( w/ generic case), where they sold the game to someone already, and didn't bother to update the store inventory.
I did manage to get all of these for decent prices through other means ( or stores), but I still peeved that those incidents still happened.
I've had a bunch of other times where you put in a hold request, and then I go to the store, and they already had sold it off. It makes the whole system pointless if Gamestop won't honor their customer's hold requests.