Continuity mistake: Right after Ryan makes breakfast for the Kents, he leans on a chair and sets the orange juice jug down twice. (00:05:35)
Continuity mistake: When Ryan gets hit by Martha's car, his comic book goes flying out of his hand. When he falls to the ground, he's holding his comic book again.
Other mistake: When Ryan gets hit by Martha's car, you can see he has both shoes on as he's going to the ground, and we never see a shoe flying through the air during the hit. Then James and Debra find the shoe in the middle of the street as they watch Martha drive off.
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