Continuity mistake: When Clark is in hospital after being thrown to land on the roof of the car his mum is helping him put a shirt on. He puts it over his right shoulder and the shot changes, his arm is all of a sudden in the sleeve.
Revealing mistake: When Clark gets hits by lightning whilst trying to save Eric, you can see that Eric is a stunt double.
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