Plot hole: Why would Danger Mouse go on the roller coaster at the end without seeing Greenback go on it first? Greenback went first in the ghost train. It also doesn't make sense that Danger Mouse would go on it when Penfold pretty much tells him flat out that it IS a trap.
Plot hole: In Russia, Soldier Boy is shown heading to the airport, He wanted to get to the US and start his revenge against his team. Problem is: he has no documentation and money to take a flight. Even if he stole the money somewhere, still would be impossible to travel without the proper documents.
The Feminum Mystique: Part 1 - S1-E5
Plot hole: If her younger sister Drusilla is sent from Paradise Island to retrieve Diana, how did she get to Washington DC or wherever, she had no way of knowing where her older sister would be.
The Night of the Raven - S2-E3
Plot hole: Antoinette is making miniature clothes for the soon-to-be shrunken West, but when West drinks the antidote to make him normal-sized, he is wearing the same clothes which would have been shredded as he grew back to normal size.
Plot hole: The episode's climax concerns Bernie rushing to the airlock to stop the rest of the crew, who are infected, from flushing themselves into space. Except that he's infected too, so they can't flush without him anyway.
Smoking Gun - S1-E2
Plot hole: Lori managed to get to the bunker through the elevator because the modern board was still replaced by the antique one. But that implies that she was able to call the elevator as normal. And if people can just call the elevator back but the normal control board has been replaced, then they wouldn't be able to use the elevator as normal, creating quite a problem in a huge hotel. Sydney earlier was not able to switch the board back to the normal one since she went out from a (mysterious?) exit/entrance, so this situation makes no sense.
Plot hole: After Kara and Alex are run off the road, Kara is convinced by "Noel Neill", revealed later to be J'onn, to stop using her powers. From context, J'onn had to have been summoned by Eliza, but in 2007, she would still think he's just Hank Henshaw; she doesn't learn he's not, or even that he's a shapeshifter, until 2016, as seen in season 1's "Myriad", well after Kara and Alex have grown up.
Plot hole: This was the first episode of the series and we see that the rangers are unable to figure out how to properly operate their zords; but in Origins Part 1 (which takes place prior to this) they have no issues with the zords at all.
Plot hole: As the first prisoner is being pulled towards the organ cutter, you see on the wall the exact shape of the body organs for the brain, lungs, heart, liver, stomach, kidneys and testicles/ovaries that serve as guides and a track for tiny saw blades to come out and cut into the person's body to harvest these organs. The problem is these are in a fixed position, which might work for some people. However people are different sizes, shapes, and heights and most wouldn't match up to these blade guides. So a good majority of the people they cut apart to harvest organs out of wouldn't even give them good ones as the blades would cut into the organs and ruin them. (00:25:20)
The White Mountains: November, 2089 AD - S1-E13
Plot hole: The main characters are being pursued by Tripods, mind controlling alien machines. My question is, if the Tripods can turn humans into 1600's puppets, complete with foxhunts, why don't they make some of said mind-controlled humans help with the pursuit?
Plot hole: Dillon was quickly identified by the city sensors as having metal parts, thus classifying him as a threat to the city. Yet Tenaya, who is essentially a cyborg, tries out for the Green Ranger without setting off the same sensors.
Suggested correction: Tenaya wasn't caught because the guards assumed the equipment was faulty. It was giving positives all day because of all the sleeper agents we find out about later.
Plot hole: In the pilot, it is established that the surface of anything/anyone made invisible by "quicksilver" is freezing. (Darien gets caught in the women's shower because the mist freezes on him. He freezes the beer mugs for the doctors.) But in later episodes, nobody notices him standing invisible - and freezing!? - next to them.
The Spores - S2-E7
Plot hole: Hal and Roy could not open the spore case with an electric power drill, but later a married couple pops it open with a hammer and chisel, then much later some children acquire the case and easily open it.
Plot hole: Skye's mother, Deborah, was held hostage by the Sixers for several years, though everyone believed she had died in an epidemic and was buried in Memorial Field. The Sixers kept her alive with medicine only they had to force Skye to act as their spy. Even though Terra Nova has a medical clinic staffed by doctors and nurses, it was never noticed that no one had witnessed Deborah dying, her body was never placed in the morgue, that was there no record of her being buried, or even questioned that there was no corpse. Deborah just disappeared without a trace and nobody wondered about it.
The Beacon - S1-E26
Plot hole: Barrows introduces himself as "Dr. Dennis Barrows," and Teddy asks, "What's a doctor?" As the isolated villagers have never heard of doctors, Teddy would have no way to know that "Doctor" was a title/profession and not simply part of Barrows' name. He should have asked, "What kind of a name is Doctor?"
Plot hole: The nuclear explosion is on Liberty Island, a small yield, but nonetheless big enough to move an enormous amount of water towards the coasts on all sides. When we see Sertrakian and the others at the harbor no water is heading their way - they should be washed away by it. (00:37:30 - 00:38:45)