Continuity mistake: When Jason starts knocking on Lana's door, the clasp from the door chain is all the way to the left. The camera cuts to Lana in bed. When it cuts back to the door, the clasp is now all the way to the right.
Continuity mistake: When Kal-El/Clark pushes Martha away her hands are down around her chest. The shot changes, as Kal-El builds up power to fly, and now Martha's hands are spread out away from her body.
Continuity mistake: While Martha reads to Jonathan, as he is in a coma, the light on his hands change. In the shot from the right side of Jonathan's bed his hands have only a normal level of light like from a small table lamp. The shot changes to look at Jonathan from the doctor's point of view and suddenly Jonathan's hands are very brightly lit like from a spotlight. No one changed or turned on any other lights between shots.
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