Audio problem: When the thief with one arm tells his other two buddies to "check this out" the shot switches to the right side of him. In that shot you can see this guy say "check this out" again.
Continuity mistake: After the encounter in the meat locker, Lex and Clark talk outside Fordman's store. As Lex turns to leave there is a truck driving down the street in Clark's direction. When the camera switches to Clark, the truck, which should be in this shot going behind Clark, is nowhere to be seen.
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