With early CDs I've heard it could be caused because of the paper insert in the front of the case. The paper can be acidic, when the case is closed it's pressed against the top of the disc and can eventually damage it. Some places say to store CD cases on edge in a bookcase like books instead of flat to prevent the booklet from sagging down onto the disc. I'm not sure how serious this type of problem is though as most CD storage racks seem to store them flat. Newer discs might be better sealed on top too.
I've found a Sega CD game with some pinholes in it, I'm not sure if it got ruined as it still played fine though I never beat the game to make sure(it's that Power Rangers game). I've also found a few PC games like that, I can't really recall coming across too many discs like that but it's not like it only happened once or twice either. I just make sure to check discs before I buy them.