Plot hole: At the start of the episode Samantha is shown putting the sniper rifle together during the start of the speech. The second time we see this scene, after getting the backstory during the rest of the show, the scene plays out that Samantha is backstage kidnapping Lois at the start of the speech. This would mean that Samantha would have to be in two places at once and she doesn't have any powers at all.
Continuity mistake: At the beginning of the episode an announcer calls Jonathan's name and he appears almost immediately. Later on we see what happens backstage and when we hear the announcer call Jonathan's name. The second time through he has time to say a few last words with Lois, go to the edge of the curtain and take a breath before he steps out on stage. The timing of the two scenes don't match.
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