Revealing mistake: When Clark gets hits by lightning whilst trying to save Eric, you can see that Eric is a stunt double.
Continuity mistake: When we first see the meteorite tattoos on Wade Mahaney, they are all green. When Clark sees Whitney's tattoo, it is plain black. It was also faded, which means it's not a fresh tattoo. Whenever Clark runs into the other guys, he feels the effects of the meteor rocks, but never when he is alone with Whitney.
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