Plot hole: When Kara realizes that Agent Loder is listening in on the conversation, she runs out to his car to stop him. She has Clark's ability of super speed which she uses to get over to Loder's car. As she runs she ends up running through a wooden fence and you can see, through the motion blur of her movement, she neither jumps over the fence or goes around it yet the fence never gets damaged from her running through it.
Plot hole: Justin's power is telekinesis, which he uses to attack the doctor at the beginning of the episode. He shows that he is targeting the doctor's hands by blacking them out on the drawing, but he has absolutely no way to see what is happening in the elevator to know the exact moment when to drop it and cut them off. (00:03:30)
Plot hole: In this episode, Pete comes across Clark's spaceship in a field, where it landed after the tornadoes hit the town during the last episode of Season 1. The Kents knew the spaceship was gone, and of course it was important that they attempt to get it back as soon as possible so it doesn't fall into the wrong hands. With Clark's speed and X-Ray vision, he should have been able to find the ship after not too long of a search (especially since it was within a few hundreds yards of a road). It seems implausible that he would not have looked for it, given its importance.
Plot hole: Outside the school, as Clark is talking to Jordan, there is a lot of people in the surrounding area. Clark looks up and sees the coach standing in the street and the car slams on its brakes to avoid hitting him, this causes the tires to screech thus drawing attention to the incident. Clark realizes that the coach is about to be hit by the car and uses his super speed to save him. Yet nobody seems to wonder how he suddenly appeared next to the coach just in the nick of time.
Plot hole: When Clark uses his heat vision to heat the metal door handle to prevent Desiree from escaping, he only heats one handle. I know that things were happening fast, but it wouldn't have taken him that much more time to heat both handles, which he should have done since there is no way he could have known that she would have tried that particular handle.
Plot hole: Though it fits the general plot of Davis always being first on scene, in the real world no on-duty paramedic drives the ambulance alone. There will always be a minimum of two EMTs per ambulance, one to drive and one to tend the patient. The only time a paramedic or other EMT will be alone is if they arrived on the scene in their own vehicle.
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