Continuity mistake: In the intro to the final scene there is no light beneath the loft doors, yet at the end of the scene during the pullout a light has appear beneath them and it switched on.
Continuity mistake: In the intro to the final scene, the top half of the loft doors are open with the bottom half being closed, yet at the end of the scene during the pullout, both the top half and the bottom half of the doors are open.
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