Plot hole: In episode 4-16: "Lucy," there is no reason for the criminals to be chasing Lucy on the ski slopes at the beginning of the episode. We learn later that she's been working with them all along; she calls Lois during the chase, and the call is part of Lucy's plan with the criminals. Lucy being chased by the criminals would make sense given the story she gives Clark during the next part of the episode, but it doesn't make sense for what we ultimately learn is the truth. And nobody from Smallville is anywhere near the ski chase, so it also doesn't make sense as any kind of a ruse.
Plot hole: During the flashback scene showing how Chloe and her father survive the house explosion it is explained that there was a team in the house and they grab Chloe and her father and rush them into a tunnel just seconds before the house explodes. However, as seen in the episode Covenant, Chloe is standing next to the door and Chloe's father is more than 15 feet away from her when the door of the house shuts. As soon as that door shuts the house explodes so unless this S.W.A.T. has Clark's super speed ability this would be very much impossible.
Plot hole: Clark is possessed by Dawn. Jonathan shows up and he has a chunk of kryptonite. Jonathan hides the kryptonite behind his back and Clark's body does not feel it until Jonathan takes the kryptonite out from behind his back. What, is Jonathon made of lead or something?
Plot hole: In the episode Onyx, Lex's alter ego holds him hostage in the wine cellar claiming that when they were kids, Lex accidentally got locked in down there. In the pilot episode, it is established that although Lionel had the castle shipped over from Scotland brick by brick and built, they never moved into it.
Plot hole: In order for Clark to push Jason out of the way of the already fired shotgun blast Clark would have to be moving much faster than the shot. Hitting Jason at this speed would have caused Jason some serious injuries. When Jason is with Lana at the Talon he has no damage from the shove.
Plot hole: When Dawn enters Clark's body, she slaps Chloe in the face with the back of the hand, and Chloe goes flying. A few minutes later, we see Chloe get up and say that she's fine. Getting backhanded by Clark would make you very far from fine. First of all, Clark can knock someone out just by tapping them on the forehead, as seen in a previous episode. Second, Dawn has no idea of Clark's powers, so she would have used way more force than she actually needed to. The amount of force inflicted from the attack should have caused fatal injuries to Chloe. There's not even a cut or bruise or anything.