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?
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?
Returning Japanese (1) - S6-E21
Plot hole: In this episode, Hank meets his paternal half brother. They look alike. However, we saw in an earlier episode that Hank's facial structure takes after his mother, not his father. Since they are paternal half brothers, then the Japanese brother cannot look like Hank since he has a different mother.
Plot hole: Pike says he doesn't want women on his bridge, Number One being the one and only exception, and he keeps ordering Colt off it. His apology to Number One indicates that A) he doesn't think of her as female, and B) she's the only exception to his rule. So how does he overlook the very female crew-woman seated at the science station? (00:06:55)
Shootout at Diablo Station - S2-E11
Plot hole: Well within earshot of the others in the small room, Curry comments to Heyes (purely for the viewers' benefit, since Heyes already knows it) that if Lom Trevors is killed, their amnesty will go with him. This information should have blown their cover, but for some strange (and unbelievable) reason, no one wonders what he's talking about. (00:19:00)
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.
Plot hole: Huge plot error: Apophis and Clorell (Skara) should not have survived the explosion in Season 2, Episode 1 (when they attack Earth with two ships). In "Family" they explain that Apophis and Clorell survived by escaping through the stargate aboard Clorell's ship moments after Daniel Jackson did the same. However, when Daniel Jackson escapes through it, Apophis and Clorell are not even on the right ship, and there is 1 second left on the C4 timer when Daniel escapes. They actually show Daniel Jackson escape, and then cut to Apophis and Clorell still aboard their ship. So apparently, Apophis was able to "ring" from his ship over to Clorell's ship, make it to the stargate room, dial an address, and escape through the stargate all within literally 1 second. Is this guy related to The Flash?
Suggested correction: That's not what happened or what was said. Daniel suggested Apophis and Klorel used the rings after he did, not that they used the Stargate after him. In "The Serpent's Lair", we see Apophis and Klorel use the rings BEFORE Daniel uses the Stargate. But we don't actually know how much time is meant to be left on the C-4 when they use the rings. They ended up using the Stargate before Daniel did and they never cut to them on board after Daniel escapes.
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.
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.
Handcuffed - S4-E18
Plot hole: Chrissy's policeman cousin informs the roommates that there was a complaint from a neighbor about her husband on his roof watching the girls dance in The Apartment with binoculars. However, when the girls were dancing, the front door was fully closed and the very thick drapes were fully closed so how could such a complaint exist?
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.
Plot hole: Ellen and Rob wear wedding rings, yet their wedding is not announced until "An Affair to Forget" in the second season.
Shift Into Turbo: Part I - S1-E1
Plot hole: Divatox and co. live in a submarine in Angel Grove lake. In "Hogday Afternoon", Angel Grove lake was drained to about 30ft at the deepest. The lake would have to be several hundred feet deep for a large submarine to hide there.
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.