This is why I rarely do LCS's.
If they were upfront with policies (limit 1-2 on new releases, actually pricing book and not waiting for the shocker / eBay check at the register) I don't think I would complain.
I have been quoted "well, that's what they are bringing on eBay."
Guess what, that's where I'll be buying them. Understocking is a problem as well (they hold #1's and such behind the counter and sit on them). All these things do is force conversations like this, pre-orders, and drives business out the door.