Continuity mistake: While Clark is chained up, Chloe uses her fingernails to dig into Clark's chest. You can see that since Clark has had his powers taken away her fingernails draw blood. In the shot of Clark screaming in pain you should see where the blood came from the scratches but there is no blood visible.
Continuity mistake: As Harry goes into the pond the second time the pylons are connected now with yellow crime scene tape when the camera is out over the water looking at Harry on the walkway. As the camera is in the water, watching Harry fall in, the pylons are gone, even though they should be in the shot, and are connected by a wire instead of crime scene tape.
Continuity mistake: When Lex first tries to break out of Belle Reve, he stabs a security guard in the leg with a pencil deep enough to draw a large amount of blood on the guy's pants leg. But when Lex is trying to incapacitate the man you can see the pencil flopping around on the guards leg and not sticking inside the guy's leg.
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.
Continuity mistake: When Clark, Pete and Chloe were searching for Clark's father in the woods, they stumble upon a motor home dropped by the tornado. Chloe then picks up a Nixon's camera and looks at it. Cut to Nixon and Jonathan Kent then back to a wide shot as we see Chloe throwing the camera down onto the ground. Clark then uses his X-ray vision once again. Cut back to a wider angle (as they walk away) yet we see Chloe throw down the camera once again.
Audio problem: In the scene where Jason and Isabelle/Lana are talking and he is about to burn the book with the lighter, she quickly grabs the book with her magic. Isabelle then says some sort of spell flinging Jason against the wall to the right. In the shot where you see him thrown against the wall, Isabelle has already said the spell, but you can see her mouth moving saying the same thing (though nothing is heard).