Exodus (2) - S2-E23
Continuity mistake: When Clark is fighting with Dr. Walden, twice Dr. Walden sends Clark flying, with his powers. Both times, when Clark hits the ground, he becomes quite buried into the soft dirt, not entirely, but relatively sunken into it. However when it will cut to the next shot, Clark is lying on the dirt without being buried into it at all. This is obviously due to switches between actor and stunt double.
Exodus (2) - S2-E23
Continuity mistake: When Kent leaves on his motorbike at the end of the episode, in a shot from behind Lana crosses her arms. In the next closeup her right arm is up by her mouth.
Exodus (2) - S2-E23
Continuity mistake: As Jor-El is first burning the mark on Clark's chest the mark moves to the upper right part of his chest. In the next shot, closer in on Clark, you can see the same area again but now there is no mark where there was one before.
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