Other mistake: Lois digs up Chloe's grave site to unearth her casket. It is obvious that the casket is not buried six feet deep. You would think, with all that is going on, that LuthorCorp would have at least buried the casket deeper to deter inquisitive eyes and maybe throw in a few scattered bones for good measure.
Other mistake: In episode 4-14: "Krypto," Genevieve tells Jason that the heirs of a 17th century woman named Gertrude are in danger. She then tells him that they themselves are "Gertrude's ancestors." But she must mean descendants, which means the opposite of ancestors.
Other mistake: When Clark is in the girl's room and a noise comes from the closet, Clark uses his X-Ray vision to see there's a person in there because he can see the skeleton and is surprised to see it's Lois when he opens the door. However, it's been shown before that Clark can use his X-Ray vision to see objects and people through solid objects. He should have been able to see that it was Lois rather than just a skeleton of an unknown person.
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