It's most likely due to being dehydrated. Just make sure he has fresh water and his humidity is at a normal range and it should return to normal after a while...
http://ball-pythons.net/forums/showt...Dented-eye-cap
http://www.ssnakess.com/forums/pytho...hon-s-eye.html
http://www.repticzone.com/forums/Bal...es/937634.html
http://www.redtailboas.com/f25/my-ba...his-eye-13157/