Continuity mistake: In the barn loft evil Lex has a kryptonite ring in a lead box. When the camera is in front of Lex he is holding the box so that the lid is pointed towards his thumb. When the camera is behind Lex the box is turned so that the lid is pointed towards the end of his fingers.
Continuity mistake: As the computer says "Subject seeds exposed to radiation" there is a camera shot showing the temperature monitor in the lower right of the shot. In that shot the readout shows the temperature reading is close to 100% of maximum. Then, in the next shot as the scientist says ".absorption level: as expected" the temperature monitor is now close to 90% as we see it climb up to the 98% they were trying for.
Continuity mistake: When Bad Lex is beating up Good Lex in the cellar right before their bodies are joined again, he repeatedly hits him on the right side of his face. However, when the two are finally fused back together, there is a bruising on the left side of Lex's face.
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