Christmas Special: Part 2 - S3-E2
Plot hole: Lee and Dawn overstay their tourist visa in the US, then fly back to the UK for the Office Christmas party. They then get into a taxi to go out to the airport in order to return to the US. They're kidding themselves. As I know (to my cost) when you overstay a tourist visa, the US Immigration Service finds out when you check in at the airport on departure. They'll be refused reentry, and probably barred from entering the US for up to six years. (I got a three year ban.) Neither Lee nor Dawn could possibly be unaware of this nor think they could beat the system as they would have been arrested when they checked in in Florida on departure (as I was), and they would have remained in small holding cells until the paperwork banning their return had been processed and their passports stamped 'Invalid for U.S. Entry', as mine was. (All this takes about seventy two hours, so they'd have missed the Christmas party anyway.) The mistake is NOT that they were able to leave the USA - that is explained (it's still not possible, but in the context of the show and the suspension of disbelief we are meant to believe it) the mistake is that they are on the way back to the airport to return. That's absurd. They would have been under no illusions as to their banned status re reentry to the USA.
Day 2: 7:00 A.M.-8:00 A.M. - S2-E24
Plot hole: Peter Kingsley is shot and killed by a man in a helicopter just as he is about to kill Jack. Kingsley would definitely have heard the helicopter approaching.
Plot hole: Season 5, episode 20 (My Lunch). One of Dr. Cox' patients needs a heart valve transplanted. Heart valves don't have to be transplanted from another person. They can be replaced by a metal valve, or the surgeon can create a new valve from a different part of the patient's body. There was no reason to wait for a donor valve when they had other options available.
Plot hole: In the start of season 4 we meet Liberty's little brother, Danny. J.T. and Manny are making fun of him because he is new to the school and is starting out. If he is starting out, then he should be in the 7th grade, because it is stated in the first episode that the school changed into a 7-12. Liberty, J.T., Manny, Emma,Toby etc. are all in the 10th grade so how does it end up that Danny is a grade below Liberty?
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.
Plot hole: Vaughan discovers Lauren is a mole when he goes through her briefcase and discovers the wig, gun and fake passport she used in Germany a few hours before - surely even the worst secret agent in the world would have enough sense to get rid of such incriminating evidence as soon as possible, and not carry it back to the USA (sneaking it onto a plane, presumably) and leaving it in the room where the man you're lying to sleeps. Lauren is a highly skilled agent, if the Covenant selected her for a mission this important, so it's out of character (without an explanation) for her to be so sloppy.