Factual error: While Clark is standing on the field at Metropolis University at the end of the episode the shot pulls back to show the entire field. As it does there are two 50 yard lines visible and the goalposts in the wrong position because it's a Canadian football field, but Metropolis University is in Kansas.
Factual error: Clark finds Lois in the sewer and decides to use his heat vision to destroy the lock of the gate that is separating them. Clark uses his heat vision on the lock and the lock explodes, this is a very minor explosion. It also causes the door to fly off the hinges. Now the explosion from the lock is odd since heat vision causes things to melt and not explode, but Clark wasn't even using the heat vision on the hinges and they are destroyed. This is inconsistent with how his heat vision has been shown to work before.
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