Continuity mistake: As Chloe and Clark talk about their feelings the shoulder protector/pad of Clark's backpack switches position with no help from Clark. At first it is more in front and showing more than a few shots later, again with no help from Clark by shifting the backpack, it is more on top of the shoulder and not as visible.
Continuity mistake: In the CG shot of the shotgun shot flying in slow motion towards the camera, the blue florescent light that was swinging in the previous shots is gone.
Continuity mistake: As Lois and Clark talk about her leaving, Clark turns to talk to her. Before he turns around the shoulder protector is between his hand and his shoulder and the red side is facing out. In the next shot, even though he made no motion to alter the position, it is now fully on his shoulder with the black side facing out.
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