Vortex (2) - S2-E1
Audio problem: When Lex talks to Clark, Clark clicks his flashlight on, and you hear the click signifying he has turned it on. But in the next shot, the flashlight is now off, without another click sound heard to signify that the flashlight was turned off.
Audio problem: After Ryan collapses at Lex's, he and Clark are talking while Ryan is in the hospital. In the shot of Clark as Ryan says "I know what's wrong with me." Ryan's mouth is visible and you can see that he is not speaking the line as we hear it.
Audio problem: After Clark is dumped into the blast furnace and the thieves make a getaway in their truck, you can hear the sound of an accelerating engine as it's driving away, but the brake lights are on.
Audio problem: Clark says "What if it's some sort of high tech crop duster or something?". Pete replies with "She'll never let us live it down." After the shot changes you can see Pete's mouth say "live it down" again with no sound coming out.
Audio problem: After they get the spaceship into Pete's shed, Pete wants to go tell Chloe. Clark insists that he doesn't and Pete says "To her, this thing is the Holy Grail.". The shot zooms in and Pete's mouth shows him saying "Holy Grail" again even though he already said it and you don't hear the words.
Audio problem: While talking about Tina Greer's suicide after Chloe says "lit a match" you can hear Pete say "okay" but you see his mouth doesn't move with the word.
Audio problem: When Whitney is tearing up the bathroom, he throws the door and we don't hear it land. I saw this on the DVD, so it was not a transmission problem.
Exodus (2) - S2-E23
Audio problem: At the wedding, after Jonathon gives Lex the compass, in a side shot we hear Jonathon say a line, yet his mouth is completely out of sync.
Audio problem: After the DCA shows Clark and Jonathan the metallic key, Clark says, "We need to think about mom," but his lips are not moving.
Skinwalker - S2-E10
Audio problem: In the barn, as Kyla and Clark talk about Skinwalkers, Clark says "like the legend of Naman is just a story?". When the shot switches to Kyla you can see Clark is talking but no dialogue is heard from him.
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