Revealing mistake: In the early scene with the baby, there are a few overhead shots of the parents and child. It is clear that in these shots a fake baby was used - he is completely motionless, even though he was moving arms and legs before and after and is crying. (00:02:00 - 00:03:15)
Revealing mistake: At the command center outside Martha is watching a monitor with the hostages on it and she asks "Where's Clark?". The next shot is one of Clark running down a hallway, inside the plant, using his super-speed. As he is running the red lights along the ceiling are revolving faster than they normally do and return to normal once Clark stops using super-speed.
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