Continuity mistake: At the beginning when Clark and Lana are on the small pier by the lake, it alternates from sunny to shady between shots during the scene.
Continuity mistake: When Clark goes to give the flowers to Sarah, her uncle answers the door. The first shot is of the uncle through a flyscreen door, which he opens. We then see a shot of Clark outside the door, and then the uncle opens the flyscreen door a second time.
Continuity mistake: When Lana undresses before jumping into the lake, she kicks all her clothes right beside Clark's feet. But in the shot where she dives off the end of the pier, all of the clothes are piled well away from Clark.
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