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: As Alicia holds the kryptonite on Clark her hand turns between shots. While she says ".but you broke the rules first." there is a camera change. Before the change the frontal view of Alicia has her holding the kryptonite with the glowing part straight up. After the camera change she is now holding it so it points to her left.
Continuity mistake: The position of Clark's sleeve to the tourniquet change between shots. When Dr. Bryce first ties the tourniquet she does so at about an inch from the end of the sleeve. In the next shot, as Clark lies unconscious and nobody touches his sleeve, the tourniquet is tied around the sleeve and no longer on his skin. Just before Dr. Bryce sticks the needle in it's back to being an inch from his sleeve.
Continuity mistake: In Episode 22- Season 5 - "Vessel": At the start, Lex wakes up and heads towards an open field many miles away from the mansion. They show a camera shot of his face in the field and the sky is grey and cloudy, but in the very next shot the sky has turned blue and the sun is shining.
Visible crew/equipment: Episode 22, Season 5 - "Vessel": Lex returns to the mansion, after being abducted, with his new powers. When he shows Lana by shooting his hand, they start talking by the stained glass window. The reflections in their eyes are supposed to be the light coming through the window, but are actually from a white screen used for lighting. The reflections in their eyes are rectangular to confirm this.
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.
Other mistake: Lex picks up a chisel and stabs Clark in the side. It bounces off and out of Lex's hand. The last couple inches are bent and twisted. Chisels are made from extremely tough steel. But no matter how hard Clark is, Lex is not strong enough to exert the force necessary to bend the chisel itself.