Plot hole: When Nixon and Jonathan are trapped in the crypt after the landslide, Nixon says he can't breathe, and Jonathan says this is because the landslide cut off the air supply. However, we can see beams of sunlight shining in. So, unless the ceiling of the crypt is made of airtight glass, that landslide didn't cut off the entire air supply.
Plot hole: Chloe says the coroner found teeth marks on the foreman's bones. During the attack, at the beginning of the episode, the foreman only got a couple of scratches on his face and the rest of his clothes were perfectly fine and hadn't, in any way, been torn up. It would have taken the wolf tearing through the clothes, through the skin and, finally, through the muscle to leave any teeth marks on the foreman's bones and that did not happen.
Plot hole: Mayor Tate and Lex have a discussion about bribes and Tate says this is his 4th term. In last season's episode "Crush", Pete gets a job as a summer intern on Mayor Spiegel's re-election campaign. So how is it possible for Tate to have been on his 4th term when in the previous year Spiegel was Mayor?
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: 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.