Im no expert and could be completely wrong but i would guess its due to stress. I saw a bunch of young ball pythons in a pet store the other day and they were in the same aquarium and one or two of them had dented eyes. so maybe you should just not handle him for a few days and make sure you keep humidity up and fresh water, and see if that helps.
I dont know about the touching the eye thing, im sure somebody will know more than me on both topics. Hope i helped a little