Continuity mistake: The field trip is supposed to be on the 39th floor, as stated by Clark and the sign next to the elevator. The view outside the large windows as Lionel is talking shows that they are no more than 5 stories up.
Continuity mistake: As Alicia holds the kryptonite on Clark her hand turns between shots. While she says ".but you broke the rules first." there is a camera change. Before the change the frontal view of Alicia has her holding the kryptonite with the glowing part straight up. After the camera change she is now holding it so it points to her left.
Continuity mistake: While Alicia is in Clark's bed she says "I know you wanted to kiss me, Clark." and while she says this her hand is on Clark's face. The very next shot shows her hand is nowhere near his face.
Continuity mistake: When Alicia confronts Lana in the Talon, when Alicia says, "you're definitely not smarter" Alicia has the knife right on Lana's cheek. When the camera switches to behind Lana, as Alicia says, "You don't have my abilities" the knife is not on her cheek.
Continuity mistake: After Adam says "Look who's talking." you can see Lana raise the notebook she found as she starts to respond when the camera is behind her. When the camera jumps to the other side, facing Lana, the notebook is down instantly between shots and she has to raise it up again.
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