Phoenix (2) - S3-E2
Plot hole: When Edge needs the vial of Clark's blood back, Edge holds Clark's parents hostage. Clark decides to use a sharp piece of kryptonite rock to cut his skin and give Edge a new sample. When Clark picks it up, and when he places the kryptonite rock on his skin, he shows no sign of the usual effects of the rock which include the green lines radiating up his arms.
Plot hole: During Clark's rescuing Lana from the fire in the basement, Clark wakes Lana just before he is grabbed by the coach. Clark then tosses the coach all the way across the room and into a wall. Lana makes no mention of how Clark could toss a full grown man across a room like that even though it happens right in front of her face.
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: 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.
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