Plot hole: If Noah could be brought back from the dead with Claire's blood why couldn't they bring back Nathan? Was turning Sylar into Nathan really the first thing they could think of?
Plot hole: The Winslows' younger daughter, Judy, disappeared from the show in 1993 (halfway through the series' run) with no explanation.
Planet of the Spiders - S11-E5
Plot hole: At the climax of episode 2, the Doctor is about to catch Lupton when the latter simply teleports to safety. So why didn't he do that in the first place, before engaging in a 15-minute chase?
Plot hole: The protagonist gets in the exclusive, multi-millionaire, invites-only auction because the invitation is on a printed letter that he faked. This means that the guards at the entrance don't have a guest list to check, and since nobody knows who this person is, the staff does run a background check on his identity when he makes the first outrageous bid...by looking his name up on Wikipedia. That's mighty low standards of security, especially for an auction that was supposed to be for a selected audience and the most important in France.
Plot hole: Throughout the show it is reported several times that Billy and Ally met when they were both eight years old in a park by sniffing each other's bottoms. However, when Billy is buried in season 3 his tombstone reads, 1968-2000, making him 32 years old. Ally is only 29 and does not turn 30 until later in that season which would at the very least, put them 2 years apart. (00:41:15)
100 Light Years From Home - S5-E19
Plot hole: At the end of the episode, Dawson is seated in the kitchen talking to Pacey in a normally loud voice. At the same time, Joey and Charlie are awake and talking in the pup tent in the living room, very close to the kitchen. Later in the Season we learn that Joey had no idea Dawson had driven down to Florida to see her, as apparently he left without seeing or talking to her. But being in such close proximity that morning; there is no way Joey would not have been able to hear Dawson's voice as he talked with Pacey. The living room was close enough to the kitchen, so it doesn't make sense that Joey wouldn't have known Dawson was there and if she did-she would have gone to talk to him.
Strawberries and Cream: Part 1 - S3-E23
Plot hole: In the heat of killing fake Red John, Jane forgot to notice that Craig O'Laughlin never knew about the mall setup to lure Red John. So definitely Gale Bertram himself was in contact with the serial killer which he may have missed first up, but all that time in jail afterwards he could have figured it out.
Plot hole: Hawkeye calls a number of people into the mess tent over the PA - the ones he allegedly suspects of being behind the thefts he is suspected of himself. Interestingly enough, Ho Jon, later revealed to be the guilty party, is not on Hawkeye's list - yet he shows up uninvited, just to be ensnared by Hawk's clever ploy. Note also that he had no way of knowing what the purpose of the meeting was, so we cannot ascribe to him the motive of wanting to find out how much Hawkeye knew.
Suggested correction: Of course Ho-Jon would come to the tent; it makes perfect sense, since he is the "houseboy" of the Swamp and, consequently, a sort of personal assistant to the Swampmen (Hawkeye, Trapper, and Spearchucker). He simply followed Trapper and Spearchucker to the tent after the announcement, probably figuring they might need him in some way.
It's late evening. It's, as far as anyone knows, an official meeting. Ho Jon isn't "standing attendance", he's sitting at the table (which is very convenient for him to hide his hands later). If he WERE standing attendance, it would be the only time in the series he does so in the mess tent instead of the swamp. It would also be the only time he's attending a meeting anyone called. Also he isn't a "house boy" - that would be totally out of character for Hawkeye, see "The Moose" - he's more an adoptee and roommate who makes himself useful. And last but not least: What a convenient coincidence, that just the guy who turns out to be the culprit would turn up uninvited, because he "might be needed" instead of staying the hell away because he is guilty and suspicious of the whole affair! Had - HAD, which he hasn't - Trapper said "Ho Jon, you better come too", you could call it a Deus Ex, but the way it is, it's just a plot hole, to quote Margaret Houlihan, "period, end of sentence."
Plot hole: Burke is murdered so that Doward will be sent out to replace him, as both hold the same rate of CPO sonar operator. But there are many CPO sonar operators in the Royal Navy. How can the GRU be so sure that Doward will be the man chosen to replace him?
The Governor's Pleasure - S3-E1
Plot hole: The governor refuses to open the door for the prisoners when they have Vera hostage, and you can hear her saying "no" "return to your units" over the radio, which Channing had to overrule. Later on in the show somehow Vera doesn't know the governor refused and has to find out from Channing. But Vera was there next to the radio the whole time. They use normal radios without earpieces so there is no way she didn't hear. (00:38:05)
Plot hole: After Rex learned that he was not really a DiMera but in fact a Brady, he suddenly became "poor." But a lot of things don't add up. Firstly, after Tony died, there was never a funeral or a will reading shown, but it seems likely that the twins would have been left something. Secondly, Rex graduated from college in the spring of 2003 and is an incredible genius who invented a laser that turns coal into diamonds. So although he might be on his own financially, he should be able to get a pretty good job without much trouble, but there's no indication that he has even tried. But Rex being poor has instead become a significant plot device, because Bonnie does not want him to marry her daughter Mimi as a direct result of it.
Plot hole: When both Gwen and Eve were in prison in January of 2005, Ethan was trying to get Theresa (whom Gwen had stabbed in the back) to drop the charge of attempted murder so that Gwen would be able to leave the prison. At the same time, Eve was being charged with three attempted murders, including that of Julian in 2001. But Julian loves Eve, and they have reconciled any differences they had three years ago, so why doesn't he also have the option to drop one charge of attempted murder?
Plot hole: When Sam and Dean realise they need to destroy the hook to stop the Hook Man, they find out that it has been reforged into something else. They state it needs to be set on fire to stop him, but if it was melted down and reforged then it has already been set on fire and the Hook Man shouldn't be latched on to it in the first place.
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.
The Promise - S3-E11
Plot hole: When Bo Jenson visits Richard Allen, he takes the elevator at the far south end of the ER wing, near the ER nurses' station, straight up to the 6th floor and then turns left to get to Richard's room in the short hallway, by the windows. When Richard jumps out the window and lands on the ledge, we see he's on the south side of Rampart's main building. Considering the actual floor plan of the hospital, this is completely impossible. The ER is located in the south lower wing and only has two floors, so Jensen could not have gone up to the 6th floor from the elevator he took.
Plot hole: Those people created for medical experiments cannot run. In fact they can barely walk, so how come they can climb nearly as fast as Rose? What's more, when you see them climbing, they seem to have little ability to coordinate hand over hand. Even with the delay brought on by the cat-woman-thing, they should not have been able to keep up with her.
Plot hole: Throughout the series, auxiliary characters are always far too willing to give all kinds of information to Tru. Doctors and registrars constantly give her privileged information about patients and students. Tru is often able to retrieve information like addresses and phone numbers from people's service and utility companies, when normally you must verify your own information before they will even talk to you about your account. Of course there can't be an episode if Tru doesn't quickly find the person who asked for her help, even though she doesn't usually know much more than their name, but it's still a bit conspicuous.