These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Bobby's little moment with Kitty - his hormones wanting an intimate moment that he's not able to have with his girlfriend? Or just doing something nice for a friend with no bad intentions or ulterior motives?
Rogue's attitude as well - does she have a legit reason to be suspicious? Or is she just paranoid and possessive?
Broken Base/Contested Sequel: The film is either a bad representation of the Phoenix Saga and a total cop-out as far as the role of Cyclops goes, and being "The Wolverine and Jean Show" and devoid of all other character development... or it is an adequate adaptation of the Phoenix Saga that does away with plot elements that would have been out of place in the established movie canon, and a sweet action movie in which all hell breaks loose and Wolverine owns the show. Take your pick.
Critical Dissonance: The film had the worst reviews but the best box office results out of the original X-Men trilogy, although a lot of that was banked on the goodwill from the first films, which were parlayed into a HUGE opening weekend for the third.
Harsher in Hindsight: After watching X-Men: First Class (which revealed that the young Xavier taught Lehnsherr how to achieve greater control over his power by finding the point between rage and serenity—the latter requires a happy memory), Magneto's line of "Charles always wanted to build bridges" as he's moving a large section of the Golden Gate Bridge seems to indicate that he's thinking about his old friend instead of his mother in order to attain serenity. And like his mother, Xavier—whom he loved as a brother—is now dead, so happy memories from their brief friendship in 1962 is all Magneto has left of him.
Hilarious in Hindsight: Kitty and Bobby's relationship being a Not What It Looks Like situation for him and Rogue. Takes on a slightly new light now that Ellen Page is open about being a lesbian. Rogue really did have nothing to worry about. Bonus point for Anna Paquin is informed to be bisexual, so is Rogue jealous on Bobby or Kitty?
The government hears that Magneto is raising an army to attack the mutant cure laboratory on Alcatraz. In response, they arm the guards there with mutant cure dart weapons in plastic dart rifles, the latter of which is sensible to stop Magneto but the former being Crippling Overspecialization at its finest. This only works because Magneto is equally stupid. They also leave Leech at Alcatraz instead of quietly moving him somewhere else when they know his life is in danger. The loss of life would still be massive, but they would have denied Magneto his prize and made sure he could never find him again.
Magneto's plan involves uprooting the Golden Gate Bridge to bring his mutant army to Alcatraz. He could have just as easily dropped the bridge on Alcatraz, removing the need for an army entirely, or flown himself to an unreachable distance and turned the entire island and its large supply of metal (rebar, pipes, etc.) into a deathtrap.
Magneto just sends his army in with no plan, using them as fodder to determine the enemy's capabilities. As he demonstrates later, he could just have his A-list destroy everyone in a few moves and they would be powerless to stop him. This essentially serves no purpose but to make Magneto seem unsympathetic.
A deleted scene does show Magneto try to get Phoenix to do something. She refuses, telling him, "You're sounding like [Xavier] again". This does not excuse him failing to use his lesser but still ridiculously powerful elites right off the bat.
Magneto is surprised that the humans are using plastic guns. This from a guy who's not only been held in a plastic prison for quite some time, but has shown the ability to detect metallic signatures from far greater distances and act on them accordingly. He does so in this very film, in fact.
Magneto controls metal. Wolverine has metal bones and Colossus turns into metal. You would think Magneto would just toss them into the ocean (something he would do in a later film), instead he leaves them on the battlefield.
The heroes need to stop Phoenix, so Wolverine is sent in to stab her with his claws. If he's in a position to get close enough to do that and you aren't going to make her vaporize his pants, then he should have grabbed some cure darts (which are literally everywhere) and cured her instead of killing her. Still psycho or not, she wouldn't be a threat.
Going with the two above, just like Magneto, Phoenix didn't sense that Wolverine was planning to kill her despite being a nigh omnipotent psychic.
Like You Would Really Do It: Magneto is stabbed with the cure. One of the movie's last pre-credits scenes shows Erik in a park, and a chess piece moves ever so slightly, implying the cure wasn't permanent. The events of the movie seem to be Ret Gone courtesy of X-Men: Days of Future Past, though. Also, in that film, Future Magneto is definitely shown to have gained his powers back.
A lot of X-Men fans blame Brett Ratner for every single problem with the film. Others blame the film's original director, Matthew Vaughn, for screwing the film over by quitting right before the start of filming, and still others hold both men equally to blame. In actual fact, while you could make legitimate criticisms about both Ratner's direction and Vaughn's decision to quit, neither of them were responsible for the storyline. That was about 90% the same as the final film well before Vaughn had signed up, and neither director was permitted to make any serious changes to the screenplay (which, despite him giving "family reasons" for his decision to quit, was apparently a major factor in Vaughn leaving the film).
Ironically, many fans actually blame Bryan Singer for everything wrong with the film. Despite (or perhaps even because of) Singer departing the franchise to direct Superman Returns, and having nothing to do with the film at all!
The whole exchange between Mystique and the guard in the prison truck.
Mystique:(posing as the President) Let me out of here! I demand that you release me! Do you know who I am? I am the President of the United States! Guard:Oh, Mr. President... Shut up! Mystique:(posing as a little girl) Why are you doing this? Let me out! I'll be a good girl! Please! Guard:(pulls out a can of mace) Keep it up...and I'll spray you in the face, bitch.
One-Scene Wonder: The movie is full of them - Vinnie Jones as Juggernaut, Eric Dane as Multiple Man, Ben Foster as Angel.
Only The Creator Does It Right: The first two X-Men films were directed by Bryan Singer. This one, directed by Brett Ratner is considered by many fans to be a step down in quality.
Scapegoat Creator: Brett Ratner picks up a lot of hate from fans of the X-Men for his role in directing this movie. Said fans tend to ignore the fact that Ratner joined the film's production at a relatively late stage (replacing Matthew Vaughn, who had been attached to direct for most of the film's development phase), thus minimizing the amount of creative input he could have possibly had to the movie.
Signature Scene: Wolverine killing Phoenix, Professor X's apparent death and the Juggernaut's "I'm the Juggernaut, bitch!" remark to Kitty Pride.
The film in general is lousy with this, wasting not only the already under-utilized Colossus, but Psylocke and Multiple Man as well. Even Callisto could have gotten more characterization mileage than simply being another of Magneto's lackeys.
Cyclops, leader of the X-Men and arguably the REAL main character of the comics: the guy was less than a cameo in the movie. The character had to deal with the death of his lover, but apparently that wasn't worth exploring, nor were his actual leadership abilities. Also, with Xavier's death, the idea of Cyke taking leadership of the X-Men as a whole and not just the field team was very doable (he's been leader of the majority of the mutants for years in the comics), and would've made sense in the context of the story. But no, he was thrown out like yesterday's trash.
Basically, there are two kinds of characters in this film: on one hand, you have the characters who could all be the poster children for this trope. On the other hand, you have Wolverine.
Scott starts hearing Jean's voice in his head, calling his name. You'd Expect: That, being the leader of the team, he would (at the very least) go talk to someone about it, especially Xavier (who would be able to read his mind and figure out what's going on). Instead: He secretly packs a bag, blows off Logan (who tries to help him) and goes off to Alkali Lake by himself. There, he accidentally(?) awakens Jean/Phoenix, who then proceeds to de-atomize him. As if acknowledging Scott's actions, no one mentions him for the rest of the film. Stuffed into the Fridge and Sudden Sequel Death Syndrome, indeed.
Prior to the events of the film (and the trilogy), Xavier implanted a series of mental mindblocks in Jean's mind to prevent a latent personality (Dark Phoenix) from taking over. You'd Expect: That anytime over the last twenty-plus years, Xavier would have at least mentioned this information to Jean for her own safety. Not even when she's brought back to the school from Alkali Lake does he bother to come down and see her (when she's feeling conflicted about her identity) and try to restore the mindblocks. Instead, he's teaching a class. Instead: Jean, more pissed off than ever, takes up residence at her old home, and Xavier willingly walks in (with Magneto, no less) to try and reason with her. It ends about as well as you would expect.
Magneto wants to kill the mutant whose DNA is being used to create the anti-mutant serum, who is located on Alcatraz Island. Magneto, in a stupendous display of power, lifts the freaking Golden Gate Bridge to get to Alcatraz. You'd Think: that since Magneto wants to kill this particular mutant, and doesn't really care about civilian casualties incurred in the process, that while he was lifting an object hundreds of feet in the air that weighs over 1000 tons, he'd just drop it on their heads or turn it into a blizzard of shrapnel to tear every living being on the island into shreds. Instead: he uses it to form a bridge, marches across it and digs in for a long, difficult, and unsuccessful siege of the place.
The Woobie: Cyclops. Plenty wanted to give him a hug during the film. And then Jean killed him.