Plot hole: When Kara realizes that Agent Loder is listening in on the conversation, she runs out to his car to stop him. She has Clark's ability of super speed which she uses to get over to Loder's car. As she runs she ends up running through a wooden fence and you can see, through the motion blur of her movement, she neither jumps over the fence or goes around it yet the fence never gets damaged from her running through it.
Factual error: When Ian throws the unconscious Chloe over the edge of the dam we see her falling down as Clark falls with her. However, Chloe's body position is unnatural for someone who is falling while unconscious. Her head/body is arched backwards when air resistance should have forced her body to become level/straight.
Continuity mistake: When Clark and Lex were talking about Helena while playing billiards, Clark picks up the stripped blue ball. They then continue to talk as he plays with the ball in his hand. He then puts it back on the table allowing it to roll but now its has changed into the cue (white) ball and the stripped blue ball can be see in the foreground right next to the side pocket and a stripped red ball.
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.
Continuity mistake: When Clark looks over to Lana, while in the coach's office, she starts to pull up her right sleeve that had slipped down. As Clark says "Lana.what are you doing here?" the shot is behind Lana and her sleeve is down and is showing a lot of her upper arm and shoulder but when the shot switches back to the front of Lana, she has her sleeve pulled up covering most of her upper arm.