Continuity mistake: When Lewis says to Lex ".the bitch that set you up." he is holding the stick with the point in his wrist. In the very next shot he is gripping the stick by the side and not from the point.
Continuity mistake: When Chloe and Lionel finish their discussion in the cave the shot focuses on the Naman/Segeth glyph and focuses through the glyph to a transition shot of an island that Lex is on. When we first see this island it is flat and covered with trees. The next time the island is shown there is now a large volcano/mountain that was not their when we first see the island.
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