Minor Plot hole: Mystique helps a bunch of mutants escape a busy Vietnam military base in a cargo plane while being disguised as an army colonel and the moment they leave she turns around and morphs into a blonde chick in front of hundreds of other soldiers and no one notices her.
Furthermore, the plan itself is pointless since Mystique didn't incapacitate or kill William Stryker who left the tent and identified the plane that the mutants took to escape. He has legal authority and could simply reorder the plane to land or prepare a nice welcoming committee for them. So Mystique’s full introduction scene served nothing.
Minor plot hole: Quicksilver puts on his headphones to listen to ‘’time in a bottle’’ on his Walkman while he dispatches the guards in the Pentagon kitchen even though the whole sequence lasts 0.005 second in real-time. Quicksilver might be lightning fast but his 1970s Sony Walkman sure as hell isn't.
Minor Plot hole: Why bring Xavier to the Pentagon if he doesn't have any powers and is literally worthless in their escape plan? Quicksilver frees Magneto, Hank jams the cameras, and Wolverine is the muscle in case of a fight, so why did Xavier show-up? He had nothing to do and everything to lose. But I guess we needed a cool scene of Magneto and Xavier meeting-up.
Minor Plot hole: Trask uses his mutant detector to spot Mystique hiding has a Vietnamese general and orders the soldiers to arrest her. The only problem is that Trask has no authority, he is not the government, he is not on American soil and he is not dealing with American citizens. Do you see a lot of dwarf tourists randomly asking for someone’s arrest based on their Toys-R-Us gadgets that no one seems to question? Yeah Mystique’s cover would eventually get blown because she speak every languages with a big American accent but it’s nonetheless retarded to see the guards and the Vietnamese generals completely agree with Trask the second his plastic toy tells them one of their brothers of war is a mutant – a concept most of them never heard of before.
Minor Plot hole: Magneto has a new power in one scene, not only can he manipulate metal, he can also separate it to the microscopic level and implement it to giant robots he never saw, in the dark, in 8 different train cars at the same time, in order to hijack their electrical components he never saw – which puts him very close to omniscience. This power was never seen before or after this scene and with good reasons.
Major Plot hole: The final scene of the movie where Wolverine wakes-up to find all his X-men alive and teaching at the school is a great scene – it’s just unfortunate that it doesn't make sense for Wolverine to wake-up in the future and not remember anything since he last drowned at the end of the movie. You see, his future consciousness was sent in his younger self to alter the past and he succeeded. This means the dark future never happened and we get to see the nice future where everyone is alive. But young Wolverine who was ‘’possessed’’ by Older Wolverine would have awaken from his incident in the 1970s without remembering anything from his past week BUT from then on, he would continue his life and the older Wolverine simply stopped to exist. It makes no sense for younger Wolverine to get a little older, become a teacher at Xavier’s school, and one day, have his consciousness murdered and replaced by Older Wolverine’s consciousness that was dormant somewhere. Older Wolverine stopped to exist the moment the past changed. We understand the need to have the audience react with amazement at the scene through the eyes of a surprised Wolverine, but it doesn't work. It’s a small cheat.
Major Plot hole: When Xavier finally decides to become useful and regain his super psychic abilities, he finds Mystique at an airport and at first tries to reason with her into not trying to kill Trask for a second time. When that fails he goes to his next and final solution: mind rape. Unfortunately, he says he can’t do it because Mystique doesn’t want to. Good call screenwriters! If mind rape is only possible when your victim wants it, it wouldn't be a very convincing mutant power don’t you think? In this film series, EVERYONE is defenseless against Xavier’s mind control EXCEPT for one guy when he puts a specific helmet on his head. If you want a conflict to be resolved logically and epically, try to not put too many over-powered protagonists in your story or we get sorry excuses of a scene like this one.
Super Plot hole: Speaking of overpowered characters, I present you Quicksilver! As witnessed from his perspective in his kitchen-fight sequence, he experiences time approximately 4000 times faster than everyone else – this is why he can dick around for one minute around guards while bullets takes almost a minute to reach their targets. The whole conflict of the movie would have been resolved if Wolverine or Xavier simply brought him with them after he helped freeing Magneto. Their plan was to catch Mystique – if only they had a time-God with them that could catch Mystique in 0.001 second and take her out of the building without anyone noticing! Screenwriting 101: you can’t introduce a character that has the perfect power to correct your protagonist’s problem and send him back to his worried mother because that’s so much more important.
And let’s go deeper. Quicksilver’s power is not to get super-fast when he wants to, he is ‘’trapped’’ in his experience of time. It is revealed by the fact that when the guards shoot at him to blow his head-off in about 0.001 second it would take for the bullets to hit him - he doesn’t need preparation time to activate his ability – it’s always on. So he always experience time super-slowly. Every conversation in his life is 4000 times slower than the rest of us. Asking for a plastic bag at the grocery store would feel like 300 hours to him. So I guess my real question is why didn’t he get crazy or try to commit suicide yet?
Super Plot hole: What’s this? Time-travel you say? Well I’m sure this won’t be a source of super plot holes like every other movie. Oh wait – let’s start:
1) Why send Wolverine in the 1970s to find Xavier and Magneto when they were enemies in order to find Mystique who is god-knows-where when they could have sent him just a few years earlier when Mystique was with Xavier AND Magneto and all of them where in the same Mansion and all friendly to each other and thus more prone to diplomacy?
2) Why wait at the last fucking second to send Wolverine back in time to alter the past if Kitty pulled that time-travelling power out of her ass more than a week ago? It’s not like the demi-god Xavier doesn't have the mental capacity to find her.
3) Why not go back in time to simply ask Xavier to Jedi-rape Bolivar Trask into liking mutants and destroying his sentinels in secret instead of just stopping Mystique from killing him? Doesn’t look like a full long-term solution. Hell, if Wolverine could convince Xavier to stop using his drugs, they wouldn’t even need Quicksilver to free Magneto from the Pentagon.
4) Wolverine is sent back in time to form a team with both Xavier and Magneto to stop Mystique from killing Trask even if both of them are completely pointless in the original task of stopping her at the Peace treaty meeting in Paris. Wolverine could just have waited for her in Paris and the outcome would have been the same.
Plot contrivance: Xavier finally re-enters his iconic Cerebro room and dusts-off a mountain of filth on his helmet that would have no-way of accumulating like this in a secret basement air-tight room.
Retroactive continuity: Wolverine meets William Stryker after the Vietnam War in his youth but X-Men Origins: Wolverine showed that Wolverine met William Stryker during the war while he was at least in his mid-forties.
Retroactive continuity: Kitty Pride has time-travelling mutant powers now for whatever reason. It’s not even a power that is somehow connected to her power of phasing through objects. She simply developed that god-like skill now even though all other mutants in the movie series never learned new powers with time.
Retroactive continuity: Hank has developed a serum in his youth that can nullify his mutation even if it is never mentioned in X-Men the last Stand where his older self is surprised to see his hand without blue fur. (But we concede that it is indeed a very good idea to retcon everything from The Last Stand).
Retroactive continuity: Wolverine needs to go back in time to stop the Sentinel program that started in the 1970s even though the sentinel program was never seen nor mentioned in the last films that covered the 1960s through the early 2000s.
Retroactive continuity: Wolverine lost his adamantium claws in the film The Wolverine and has them magically back on in the future. Did Magneto cover his bone-claws with new adamantium?
Unaddressed Issue: If Mystique can change her body mass to adapt to any form like Tyrion Lannister with a porn stache, why doesn't she always fight as a 7-foot-tall UFC fighter every time she has to punch people?
Unaddressed Issue: Why didn’t the U.S. Senate buy the Sentinel prototypes for other types of war? They might not feel mutants are a threat, but as far as we know it’s still the Cold War and I’m sure the United States Army would love to have unmanned killer-robots in the 1970s to fight communism. There is simply no way Trask’s awesome war invention would not have been bought by the American government.
Unaddressed Issue: I’m really curious to know how Bolivar Trask in the 1970s was able to make 15-foot-tall robots with plane reactors in their chests and chain-guns in their arms without any metal. I mean, it would be a marvel of science and engineering if they were in metal right now, but they get a plastic eco-friendly version in the 1970s; just give him the Nobel price of Everything and call it a day.
Unaddressed Issue: Why didn’t Magneto simply use his robots to kill everyone at the White House in front of the camera crews to establish that using robots is a bad idea, completely shut-down the Mutant fear and never exposing himself? Flying with a baseball stadium is pretty cool too but a lot less logical and a lot more dangerous for him.