Continuity mistake: There are several close up shots of the syringe that Dr. Hamilton is using to threaten Pete with and you can see that it is made of plastic. Clark uses his heat vision to overheat the syringe causing it to burst but the sound the syringe makes when it bursts is that of a glass syringe and not the plastic one he was actually using.
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: Clark tries to talk to Pete into helping him find his ship. As Clark was talking about the driver, we see the cover to Pete's locker in the foreground. Cut to a different angle and now Pete's left hand is on the locker and it wasn't there in the previous angle.
Continuity mistake: When Dr. Hamilton was about to pour liquid kryptonite on Clark, Pete hits him on the back and he goes crashing onto a table knocking everything on it off the table. Yet later we see an open bottle of liquid kryptonite on the edge of the table (which was cleared by the doctor earlier) dripping onto the doctors forehead.
Plot hole: In this episode, Pete comes across Clark's spaceship in a field, where it landed after the tornadoes hit the town during the last episode of Season 1. The Kents knew the spaceship was gone, and of course it was important that they attempt to get it back as soon as possible so it doesn't fall into the wrong hands. With Clark's speed and x-ray vision, he should have been able to find the ship after not too long of a search (especially since it was within a few hundreds yards of a road). It seems implausible that he would not have looked for it, given its importance.