Continuity mistake: Lana looks over the edge of the crater and there is a fire right in front of her on the inside rim of the crater. When the shot changes and pans up to an overhead view of the crater and ship that fire is missing.
Continuity mistake: Clark had been wearing his cap and gown for a while. When he takes them off while coming off stage the blue shirt he has on underneath has fresh raindrops on it like he had only put the cap and gown on a few minutes before the shot.
Continuity mistake: The raindrops on Clark's shirt disappear and reappear between shots. Clark's shirt is dry when he turns to Chloe and asks "I'm not normal?" but before and after this his shirt has raindrops on it. This happens again a few moments later as Lois starts to talk about "panicking in times of crisis", Clark turns towards Lois and his shirt is dry.
Revealing mistake: As the helicopter that Lana is in dodges the falling meteors in mid-air, the camera shot focuses in on the cockpit. If you watch Lana's position as she first starts to appear she is semi-transparent and the frame of the window behind her is visible through her body.
Continuity mistake: Jason Teague arrives at the Kent farm. He fires a shot into the windshield of the Kent's truck. So we obviously know the gun is loaded. Later, inside the Kent's house, Jason still has Jonathan and Martha held hostage. After Jason mentions the symbols burned into the field Martha says she doesn't know what he is talking about. Jason gets upset and racks the shotgun but when he does no shotgun shell, used or unused, is ejected. Now Jason would have had to keep the gun loaded while moving Jonathan and Martha back to the house as he would have had no time to unload and reload his gun.
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