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.DavidK93
Plot hole: Chloe writes her phone number on Sean's hand. It disappears when we see him struggling against the ice of the lake, then reappears in the scene where he is calling old girlfriends. And how exactly would pen ink survive several hours submerged in water and then another eight hours of normal activity without becoming blurred? (00:04:15 - 00:19:50)Phoenix
Plot hole: During the flashback scene showing how Chloe and her father survive the house explosion it is explained that there was a team in the house and they grab Chloe and her father and rush them into a tunnel just seconds before the house explodes. However, as seen in the episode Covenant, Chloe is standing next to the door and Chloe's father is more than 15 feet away from her when the door of the house shuts. As soon as that door shuts the house explodes so unless this S.W.A.T. has Clark's super speed ability this would be very much impossible.
Plot hole: When Edge needs the vial of Clark's blood back, Edge holds Clark's parents hostage. Clark decides to use a sharp piece of kryptonite rock to cut his skin and give Edge a new sample. When Clark picks it up, and when he places the kryptonite rock on his skin, he shows no sign of the usual effects of the rock which include the green lines radiating up his arms.
Plot hole: When Nixon and Jonathan are trapped in the crypt after the landslide, Nixon says he can't breathe, and Jonathan says this is because the landslide cut off the air supply. However, we can see beams of sunlight shining in. So, unless the ceiling of the crypt is made of airtight glass, that landslide didn't cut off the entire air supply.
Plot hole: Clark is crippled throughout much of the episode due to there being kryptonite in the tunnels. At one point he gets a rock stuck in his arm and he bleeds from this wound. For much of the time after this he has blood running down his arm from this wound. After he gets out of the tunnel he is healed but the problem is the blood from the wound also disappears. The actual wound should have healed up but the blood from that wound should still be shown staining his arm.
Plot hole: Clark uses his x-ray vision to see the remains of the girl in the wall, which seems to establish the wall is not made with lead. However, he only reacts to the Kryptonite bracelet inside until he is aware it is there, despite the fact he should have been able to feel its effects long before that.
Plot hole: Chloe says the coroner found teeth marks on the foreman's bones. During the attack, at the beginning of the episode, the foreman only got a couple of scratches on his face and the rest of his clothes were perfectly fine and hadn't, in any way, been torn up. It would have taken the wolf tearing through the clothes, through the skin and, finally, through the muscle to leave any teeth marks on the foreman's bones and that did not happen.
Plot hole: At the start of the episode Samantha is shown putting the sniper rifle together during the start of the speech. The second time we see this scene, after getting the backstory during the rest of the show, the scene plays out that Samantha is backstage kidnapping Lois at the start of the speech. This would mean that Samantha would have to be in two places at once and she doesn't have any powers at all.
Plot hole: Mayor Tate and Lex have a discussion about bribes and Tate says this is his 4th term. In last season's episode "Crush", Pete gets a job as a summer intern on Mayor Spiegel's re-election campaign. So how is it possible for Tate to have been on his 4th term when in the previous year Spiegel was Mayor?
Plot hole: Chloe has to use Lex's thumbprint to access the safe inside level 3. She gets his fingerprints by lifting it off of the flashlight he picked up for her earlier in the caves. The problem is when Lex picked up the flashlight and gave it to Chloe he had only touched the back half of the flashlight, but when Chloe lifts Lex's print she gets it from the opposite end. Since Lex did not touch that end there should be no fingerprints for her to lift and use on the security door.
Plot hole: During Clark's rescuing Lana from the fire in the basement, Clark wakes Lana just before he is grabbed by the coach. Clark then tosses the coach all the way across the room and into a wall. Lana makes no mention of how Clark could toss a full grown man across a room like that even though it happens right in front of her face.
Plot hole: Clark is delivering presents for Chloe. In the overhead shots looking down on Metropolis he super speeds from building to building and he only spends like one second in each building before going to the next one. This doesn't match what is shown while we see him leave presents by the various trees inside the apartments. In those interior shots he spends 5-10 seconds in each room. The overhead shots are not sped up. Not only do these times not match up but he would also be slowed down to open the doors or he would constantly be breaking them down.
Plot hole: In the episode Onyx, Lex's alter ego holds him hostage in the wine cellar claiming that when they were kids, Lex accidentally got locked in down there. In the pilot episode, it is established that although Lionel had the castle shipped over from Scotland brick by brick and built, they never moved into it.