Visible crew/equipment: As Clark is ambushed inside Belle Reve, in shots focusing on Lex as he is being beaten by the twin and again a few seconds later, there is a dark object in the upper right corner of the shot. There is nothing in this scene to explain it and it moves with the camera so it is probably some piece of filming equipment. Regardless of what it is, it should not be in the shot.
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: After Clark gets his powers back the cut on his cheek heals and leaves only blood on his cheek. While still at the power generator he goes to wipe this blood off of his face with the back of his hand only in the shot just before you see his hand go to wipe, a second before his hand actually appears on screen, the blood that was on his cheek is now gone as if it was already cleaned.