Plot hole: Chloe writes her phone number on Sean's hand. It disappears when we see him struggling against the ice of the lake, then reappears in the scene where he is calling old girlfriends. And how exactly would pen ink survive several hours submerged in water and then another eight hours of normal activity without becoming blurred? (00:04:15 - 00:19:50)
Plot hole: Justin's power is telekinesis, which he uses to attack the doctor at the beginning of the episode. He shows that he is targeting the doctor's hands by blacking them out on the drawing, but he has absolutely no way to see what is happening in the elevator to know the exact moment when to drop it and cut them off. (00:03:30)
Answer: The kryptonite only creates mutations when it reacts with the environment and an individual. Remember, the FDA and several environmental groups did check out Smallville after the meteor shower, but found no danger in the rocks. Obviously they're not always emitting mutating rays, or all the flora and fauna of the surrounding area would be horribly mutated.
Phoenix