As far as I know, caves are empty. I think a good way to counter players having free access to caves and all the ore would be to add spiders.
The spiders would be the size of a player, pale white, and have glowing eyes. Spiders are afraid of light and will not go near torches unless there are several spiders in a group. There could also be a spider nest structure underground where a lot of spiders spawn. The nest would have a ton of webs and would also have a treasure chest as a reward for killing all the spiders.