Plot hole: Columbo is in the Pauley's hotel room trying to figure out how the bottle landed upright next to his body after he was shot. Devlin - the murderer - turns up unannounced and uninvited. How did Devlin explain that he knew where the victim was staying when he was murdered? Media reports might have mentioned the name of the hotel but there is no way they would have included the room number.
Plot hole: A central plot device in this episode is that there is no six letter word made up of the letters EXVIN, so the murdered man cheats at the word game by playing a word he knew to be inadmissible - exvin, a wine connoisseur who no longer drinks. Since he is supposed to be a stone cold killer player at this word game, don't you think he would have thought of Vixen? Sara Sidle points that word out later - why wouldn't a world champion word game player have figured it out, using a safe, common word and avoiding a possible challenge?
Plot hole: Gretchen, Lincoln, and Sophia were able to visit Scofield and Whistler in Sona without Gretchen being recognized. She was taken in for questioning in episode 9, but she managed to escape and kill General Zavala and one other guard. The other guards knew that she was the one who killed Zavala but she was still able to sign in for visitation.
Plot hole: At the end of this episode Red takes off his shirt revealing his burned back, which leaves us to think that he might be Elizabeth's dad. However, this particular mark should have been noticed and written down in Red's prisoner file when he was taken into custody the first time (Episode 1). In that case Elizabeth would already know that Red is burned and could have asked some questions about it.
Plot hole: The very ending scene where Peter (in this version died in the ice as a boy so Walter's wife never met him) takes off some of the dust covers then picks up a toy airplane. The toy airplane he got as a child from ... Walter's wife when she was trying to placate him in an earlier episode for trying to run "home". This toy airplane wouldn't have been his as a child in this version of the universe. (00:42:00)
Plot hole: Can't fault this massive plot hole to the adaptation, but to the source material; the culprit (forgetting the stupidity of writing an incriminating letter detailing the plan to murder someone, and put it in a desk he shares with her) since there are people outside the room that are about to enter, tears the letter in 3 neat vertical strips, rolls them, puts them in the vase on the mantlepiece, and then opens the side door to slip away...instead of simply pocketing the letter and going through that same door. Nobody was going to search him or anything and could have burned it, torn it into confetti, anything, later. It takes way way longer to do what he did, which needed him to stay there in the room increasing the chances of being found out. And of course he and his accomplice do not retrieve the letter after.
Plot hole: Hippolyta tells Hawkgirl of Aresia's background of being born in the outside world, the war in her country and right up to her drifting to the shores of Themyscira. It would be impossible for her to know anything of Aresia's background as in part two, it's explained that the captain of the ship who saved Aresia died shortly after reaching Themyscira and therefore would not have been able to tell Hippolyta anything.
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: 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: After Storm's attempt to escape the Genoshan prison is thwarted, she ends up in the ocean right at the shoreline of the beach, where she is captured by a Sentinel. Aside from the fact that it makes no sense for a Sentinel to be hiding in the ocean in the event that a mutant tries to escape the prison, there is absolutely no way that a two-story tall robot could hide in the ocean right by the beach, as the water would be way too shallow. You can even see that the water level only goes up to the Sentinel's ankle area when it is standing upright in the ocean. (00:03:15)
Plot hole: The CSIs catch a murder suspect putting down a drink can when reviewing security footage of a robbery, and immediately realise they didn't see it at the scene so assume one of the first cops on the scene must have removed it. Thing is though, the murderers shot out the security camera before the actual shooting occurred, meaning there was loads of time off-camera for the killers to take the can with them, but the CSIs never even consider this - they jump to the conclusion a cop took it even though there's no actual evidence for that.
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.