Continuity mistake: There are several close up shots of the syringe that Dr. Hamilton is using to threaten Pete with and you can see that it is made of plastic. Clark uses his heat vision to overheat the syringe causing it to burst but the sound the syringe makes when it bursts is that of a glass syringe and not the plastic one he was actually using.
Continuity mistake: Clark tries to talk to Pete into helping him find his ship. As Clark was talking about the driver, we see the cover to Pete's locker in the foreground. Cut to a different angle and now Pete's left hand is on the locker and it wasn't there in the previous angle.
Continuity mistake: When Dr. Hamilton was about to pour liquid kryptonite on Clark, Pete hits him on the back and he goes crashing onto a table knocking everything on it off the table. Yet later we see an open bottle of liquid kryptonite on the edge of the table (which was cleared by the doctor earlier) dripping onto the doctors forehead.
Continuity mistake: At the collision, Pete looks out over the cornfield and sees the flashing turn signal of the truck but not its headlights, which should be brighter. (00:03:20)
Continuity mistake: After Pete confronts Clark about the missing space ship in his tool shed, Pete gets into his car and we see Clark put his right hand on the door of Pete's car. Cut to a different angle as Pete drives away but now Clark's hand is no longer on the door.
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