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.
Phoenix (2) - S3-E2
Continuity mistake: As Morgan Edge hands Lionel the bag with the mason jar of blood the camera is on Lionel's side and bag has a very neatly folded flap to keep the top closed. As Lionel takes the bag, while the camera is on Edge's side, the opening is wrinkled and not folded shut as it was before.
Phoenix (2) - S3-E2
Continuity mistake: When Clark and Jonathan return home, Jonathan collapses on the couch. It shows Clark rushing to his side. But in the next shot where it shows Martha's reaction, you can see Clark rushing to his side again.
Phoenix (2) - S3-E2
Continuity mistake: When Lex pulls the gun on Linoel, when the camera is on Lex he is pointing the gun in Lionel's face. When the camera is on Lionel, Lex is pointing the gun in Lionel's chest.
Phoenix (2) - S3-E2
Revealing mistake: When Clark rips the door off the Lincoln, you can see there's no interior panel or door glass.
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