Other mistake: Lois digs up Chloe's grave site to unearth her casket. It is obvious that the casket is not buried six feet deep. You would think, with all that is going on, that LuthorCorp would have at least buried the casket deeper to deter inquisitive eyes and maybe throw in a few scattered bones for good measure.
Visible crew/equipment: When Clark finds Lex in the Luthor mansion, they walk down the hall and into a new room. As they enter, as Lex is saying "So, hows the new ride?" if you look in the bottom left of the screen you can see a white tape marker on the floor, where Lex will walk over to subsequently. (00:33:10)
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.