Plot hole: In episode 4-16: "Lucy," there is no reason for the criminals to be chasing Lucy on the ski slopes at the beginning of the episode. We learn later that she's been working with them all along; she calls Lois during the chase, and the call is part of Lucy's plan with the criminals. Lucy being chased by the criminals would make sense given the story she gives Clark during the next part of the episode, but it doesn't make sense for what we ultimately learn is the truth. And nobody from Smallville is anywhere near the ski chase, so it also doesn't make sense as any kind of a ruse.
Continuity mistake: As Clark first gets to the bridge at Cherry Hill, the shadows establish the time as either early morning or early evening since the shadows are long. In several shots during this scene the sun suddenly jumps to around noon as the bridge shadow goes from sticking out far to one side to being almost directly under the bridge and the shadow of the semi shortens when Clark is making his super jump.
Visible crew/equipment: Just after Becker starts to chase Lucy there is a shot looking up the hill towards the lodge where she started skiing from. To Lucy's left you can see a fresh pair of ski tracks being made by whatever the camera is on. You can tell these are fresh tracks because there is fresh snow being kicked in the air because of them.
Revealing mistake: As Clark is chasing after the semi-truck with Lois and Lucy in the trailer you can see the Rocky Mountains in the background. Kansas doesn't have mountains. However, Vancouver, where the show is actually shot is home to part of the Canadian Rockies.
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