Continuity mistake: After Lionel and Professor Willowbrook finish talking Clark shows up to talk to the professor. As they talk, while the camera is behind Prof. Willowbrook, he has bright sunshine on his suit coat. When the camera is behind Clark the light on Prof. Willowbrook's right shoulder is gone.
Continuity mistake: When Clark sees that Jeremiah is in the loft, Clark stands up and closes the book he was reading as he says "What are you doing here?". The very next shot from behind Clark shows that the book is back to being open.
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