Transference - S4-E6
Continuity mistake: As Lionel's cellmate tells Lionel "I've always kind of had a thing for pattern recognition." the shot changes mid-sentence. Between changes Lionel's cellmate goes from having his arms crossed, hands holding his elbows, to having his hands almost clasped together.
Transference - S4-E6
Continuity mistake: Martha visits Lionel in prison not knowing Lionel is actually Clark. As she says "I'm only here because you told me it had to do with the safety of my son." the camera changes. Between changes, as Martha says "you", her left hand goes from being under the table to instantly being on top of the table.
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