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)
Continuity mistake: When Sean emerges from the lake and goes to the campfire, his clothes are completely dry despite the fact that he was totally underwater for hours. (00:04:50)
Continuity mistake: When Sean is in the nurses office, having his temperature taken, the light on his left side is on. After the nurse wants to retake the temperature the light is now off.
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