Other mistake: In the opening credits of the original broadcast, Kristin Kreuk's first name is misspelled as "Kristen." The credits sequence, which was new for Season 5, was corrected by the time the second episode of the season aired.
Continuity mistake: The blood on Lana's face is different then how it was in the previous episode. While at the crater in Commencement she has two distinct lines of blood on her face. One on her left cheek is thick and the one on the right cheek goes down past her lips. While at the crater in this episode the left line is then while the right line is shorter. These two scenes should be identical since Arrival picks up right after Commencement.
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