Vortex (2) - S2-E1
Plot hole: When Nixon and Jonathan are trapped in the crypt after the landslide, Nixon says he can't breathe, and Jonathan says this is because the landslide cut off the air supply. However, we can see beams of sunlight shining in. So, unless the ceiling of the crypt is made of airtight glass, that landslide didn't cut off the entire air supply.
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