I know that this occurs, usually it doesn't bother me because I'm not interested in any variants. Sometime before my first LCS closed down it charged 25 cents for the lantern corps rings that were supposed to come free with the comics. I didn't mind because it wasn't much and I really loved that store. I went to my current LCS to get one villains month book, the only one I'm interested in for the whole month (not counting Forever Evil) just because it sort of ties into a title I'm reading. None of the $2.99 ones were on the shelves and won't be in for a little while.
They did have the special covers. Since I'm not getting many comics spending another dollar wouldn't be too bad. Only they are charging $12 and up for the special covers. I noticed a few of the older covers are apparently selling for at least $25. This is especially ridiculous because I can literally get these covers online for the cover price. Actually at some online places I can get them 10-20% cheaper. Most variants online are usually marked up but not most of these (I heard Harley Quinn was but I can't say if it's true since I don't see it listed.) It's really annoying and makes me want to shop online instead of waiting for them to get the $2.99 shipment. Especially since I only try to make one trip that way a month since it is a bit out of the way.