Audio problem: Clark is upset over the death of Alicia and is in the barn loft bouncing a ball off the wall. His parents come up and Jonathan sits next to him and tells him that what happened was not Clark's fault. The very next shot shows Martha sitting down and you hear Clark throw the ball again but you can see that his hands never make and motion to correspond with that action.
Continuity mistake: Alicia's hair keeps changing as Clark holds her in his arms. In some shots the hair on her right side is messy. When the shot switches to a close up, her hair becomes neatly combed and tucked behind her ear. All of this occurs after Clark burns the rope she was hanging by.
Revealing mistake: When Jason breaks into the bathroom to rescue Lana we see a shot of the shower from Jason's POV. In that shot you can see the steam is coming from the other side of the tub and is flowing up and in. If it had been actual steam it would go from inside the tub 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