Revealing mistake: When Lucy plays her violin in Lex's mansion, it's obvious the actress isn't actually playing - her fingers aren't moving and the box is out of time with the music.
Plot hole: In the episode Onyx, Lex's alter ego holds him hostage in the wine cellar claiming that when they were kids, Lex accidentally got locked in down there. In the pilot episode, it is established that although Lionel had the castle shipped over from Scotland brick by brick and built, they never moved into it.
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