Revealing mistake: When the gas pipe explodes at the beginning before the credits, the camera goes to an aerial view. You can see that the explosion started from behind the gas pipes. (00:01:50)
Continuity mistake: As Chloe leaves Clark calls out her name. In the shot from Chloe's side of the room, Clark is holding the pitchfork horizontally low in front of him. The shot switches, as Chloe finishes her turn, and now Clark is holding the pitchfork with his arm bent so that the pitchfork is no longer low in front of his waist.
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