Phoenix (2) - S3-E2
Plot hole: When Edge needs the vial of Clark's blood back, Edge holds Clark's parents hostage. Clark decides to use a sharp piece of kryptonite rock to cut his skin and give Edge a new sample. When Clark picks it up, and when he places the kryptonite rock on his skin, he shows no sign of the usual effects of the rock which include the green lines radiating up his arms.
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