Continuity mistake: When Amy is introduced, she is writing about two lines down from the top of the page in her journal. After Troy snatches it, the writing runs about halfway down the page. (00:00:35)
Continuity mistake: As Victoria is being drowned in the bathtub, she appears very deep in underwater shots and only a few inches down in overhead shots. (00:26:00)
Revealing mistake: Once Victoria has drawn her bath, we see her get in, and then lean back into the water. However she is already wet on her chest and her hair is damp already. This is probably due to previous takes of the same scene.
Continuity mistake: At the beginning, when Seth picks up the barbell to beat Troy with, Troy is at the end of the locker room with the showers. As Pete and Clark show up, Troy is at the other end of the locker room.
Continuity mistake: When Jonathan is sitting down, before he tells Clark that he can't always be honest, in the shot from the other side of the table Jonathan is holding a book in his right hand as he is sitting down. When the shot switches to Clark's right, Jonathan is still starting to sit but now the book is in his left hand.
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