
Plot hole: As shown when Robin comes under the influence of Slade's mind control device, the hypnotized people retain their abilities and higher intelligence, just with a loyalty to Slade. That being said, when Slade hypnotizes all the DC heroes, Superman and The Flash are among them in the theater. Slade orders all the heroes to chase after and destroy the Teen Titans. The Titans take off on foot with the others running after them and are able to keep their distance in a big chase sequence. Superman and The Flash never use their super speed to over take the Titans, which would have been so very easy.

Plot hole: When (future) Agent J and (future) Boris are fighting on top of the large red docking station for the spaceship, Agent J gets shot deliberately by Boris and jumps off the edge of the dock. Then he uses his time travel device to go back in time a few seconds earlier to be able to dodge the shots. There are a few mistakes in this part. 1) There should be another Agent J and Boris there too, as they have gone back in time to that moment again. However in the movie there are only two of them. 2) The injuries sustained by Agent J (the bone spikes in his abdomen) should have remained there when he went back in time. If it were true that you healed once you went back in time into the condition you were in at that moment, then Boris should have grown an arm back when he went back in time. 3) Due to the time loop, Agent J remembers how to dodge the shots, while Boris doesn't remember anything and is surprised by the outcome. (01:29:00 - 01:30:10)

Plot hole: Spoiler. Agent M points out as highly suspicious that the twin assassins knew the location of Vungus, and High T backs her up on this, saying that only a handful of MIB officers could have leaked that information. High T also established that those aliens were part of the Hive collective. It turned out that they were not part of the Hive, and the Hive connection was made-up entirely by the villain himself...which is the Hive! What he did was absurdly counterproductive to his cause: nothing except the report he himself made up connected the Hive at all with the case.
Suggested correction: Maybe a wrong move by High T but more like a character mistake rather than a movie mistake. High T was trying to scare the agents into overreacting to what was perceived as a high risk threat. Then it backfired on him but definitively non a plot hole.
I don't mind the proposed changes of category, or even a 'demotion' to Stupidity. But I say it's more of a Plot Hole by the definition used in the website; " Events or character decisions which only exist to benefit the plot, rather than making sense." The whole plot moves along thanks to a deliberate decision by the villain who literally fabricates evidence to implicate himself.
Sorry but it COULD make sense. We have 2 aliens from planet X (which is presumed to be a "hive" territory) that - at that point in the movie - are perceived as killers. It makes a lot of sense for HighT to reinforce in Agent H and Agent M the fear of an incoming invasion by waving the Hive scare flag in front of them. HighT could not have predicted at that point in time that the twins would say "we need that weapon for the hive" before being obliterated, Thus starting a doubt in H and M.
I fail to see why it makes sense for him to tip them off about the much larger intergalactic invasion when he just needs to send them on a wild goose chase to buy himself time for the last part of the plan. He amply demonstrates that he can fake anything about their background. Or simply not fake anything at all;they have no Hive contamination, and so they are just refugees from a dead planet. Instead, he fakes evidence that implicates his faction and is caught hiding that forgery.
Maybe Stupidity is more appropriate.

Plot hole: Sam sent a post card from the church where the keys are used. But Sam was captured moments after locating the book that gives the clue about the church, and would never have had a chance to go there.

Plot hole: As the island is sinking you can see parts break off, like the island is falling apart, but if it does this every 70 years then there wouldn't be an island. It should have completely fallen apart hundreds of years ago.

Plot hole: When Magneto lands the bridge between San Francisco and Alcatraz, only the ends of the bridge are on land, with the rest still suspended in the air despite having nothing to keep it there. Magneto could arguably be using his powers to keep it supported, but at the moment he loses his powers it still does not collapse at the center.

Plot hole: While the pair are duelling on Kajimi, Kylo Ren only realises Rey is onboard his ship when the mask of Darth Vader is force-teleported between them. However in this same fight Rey is wielding the dagger, which Kylo must have known was also inside Ren's chambers before the fight. So he should've been able to determine Rey's location earlier.
Suggested correction: While he should have had some idea, it doesn't prove she is in his quarters, only that she has been there. It's also a small item that he may not have noticed in her hand, focusing more on her lightsaber.
Hogwash. He could have easily noticed it, even if he was focused on her lightsaber. Maybe it is small but rather easily noticeable.
I think the biggest point is the mask proves her location whilst the dagger in her hand doesn't.
It's also a weapon. In a combat situation a trained fighter like Kylo would have checked her other hand for a weapon as it is a common tactic to check a swipe with the main blade and stab with an off hand short weapon.

Plot hole: When you see the shot of New York, just before the scene where the apartment lights go out, there are no lights on in the buildings, or car lights in the street, although it is dark. The lights should still be on as there has not been a power outage. (01:28:00)

Plot hole: Right after the Joker goes into the cathedral with Vicky, Batman follows him with no one else entering in between the two parties. How then did Joker's goons get to the top of the cathedral before Batman or the chopper? They couldn't have planned it since Joker had to tell them where to pick him up, and they didn't know he would chase after Vicky to that particular location.

Plot hole: The only reason Kate is brought onto Matt's team is to give the CIA legal authority to operate on US soil. Given that he already has DEA agents and US Marshals on the team, all of whom seem to be fully aware of what he is doing and have no problem with it, this doesn't make a great deal of sense. Her idealism makes her a poor choice for the sort of operations the team is doing, and there are already domestic US agents available.

Plot hole: In the first night that Nyah is in Ambrose's house she meets with Ethan outside the house and they talk for about 1 1/2 min. Then we find out "Ethan" was really Ambrose with one of those "high-tech" masks. My question...After being in bed with both, how come Nyah didn't recognise Ambrose is about 5 inches taller than Ethan?

Plot hole: Now why the heck is one of the stealth fighters anywhere near the train? Stealth fighters use advanced targeting and do not need to be anywhere near their target, yet in the movie the one fighter is so close to the train when it gets blown up that it looks like it's on a collision course.

Plot hole: The Americans allegedly landed at Manchester on their way to kill the male Dragon in London. London is due south of Manchester. Why then did they head in the complete opposite direction to Northumberland?

Plot hole: When they are on the subway train, they are talking about the worm and the virus. They said that everything would happen on the 14th. A couple of scenes later, when they are setting up for the traffic lights to go crazy at 9:00, Dade looks at his watch. You can see the date as 10-18, which is 4 days afterwards. (01:17:15 - 01:22:50)

Plot hole: Peyton had his face burned in the explosion. In fact, he basically lost his lips, so he should not be able to talk very easily. While he could probably learn to speak normally again through other movements with his mouth and tongue, he does so too quickly to make logical sense. And his uncanny ability to almost perfectly mimic his enemies could probably be learned over time, but again is too quick to make sense.

Plot hole: Why would Madison Lee put the bomb in the car if she was so convinced that the Angels were dead? If she wanted to off them just in case, she could have shot them while they were unconscious. (01:21:50)

Plot hole: There are numerous problems with the final solution to putting out multiple burning floors of a skyscraper by blowing the water tanks under the roof. Blowing the floor under the tanks only channels the water into the Promanade Room. From there it cascades out the windows and - as we see in the film - falls to the ground without touching the fires on the lower floors. A tiny percentage makes it into the stairwell door and elevator shaft, despite the fact that the elevator doors were closed. All of the stairwell and elevator doors in the building were shut; none of this water makes it to the fire. Also, as we see the flames going out from all the floors no water is coming out of any of those windows, proving that the fires are going out without any water.

Plot hole: The Kaiju's EMP fries all electrical circuits next to him, and affects the base as well. If that's true, how did the helicopters carrying Gypsy survive the blast without having their electronics fried? EMP pulses induce current in all electronics regardless of whether they're powered on or not. (01:18:00)