In a ridiculously inaccurate negative review by Stephen Hunter of The Washington Post it quickly became clear that he did not bother to watch the movie, or was distracted for most of its length. At one point, he said that Rogue had the power to reverse time, even going so far as to call her "the Mistress of Rewind." He was apparently confused by the scenes in which she extinguishes flames (using Pyro's power) and makes Wolverine's wounds reappear (he let her borrow his Healing Factor. His wounds reappearing is another problem) note The wounds reappearing may not have been strictly an ontological inertia problem. For instance scurvy can cause the reopening of even extremely old wounds that have been long-healed. Wolverine may have been experiencing a similar effect with the loss of his healing factor.
A review in the Irish Times complained that a character who had been killed in the first film was somehow alive in the second... except he wasn't: Mystique the shapeshifter had taken his place. This was not only pointed out explicitly in the first film (for those viewers too sleepy to notice the characteristic flash of yellow eyes) but was a pivotal plot point in the second, which makes you wonder if the reviewer actually bothered to watch the film.
One TIME magazine profile of Alan Cumming described him as playing a "mutant villain". As in, Nightcrawler. Granted, it's an easy mistake to make if you only read the Wikipedia article on the movie, in which the first sentence of the plot summary reads, "Nightcrawler, a teleporting mutant, attempts to assassinate the President of the United States," and (as of this writing) doesn't actually explain that he was Brainwashed and Crazy even if you read on from there. Perhaps they should have bypassed the question of which side he was on and just pointed out that he spent up to nine hours getting the makeup put on him, which would be the only interesting part to someone who hadn't seen the movie anyway.
Deleted Role: The film was meant to feature brief cameos from Beast and Gambit during the brainwashed Professor X's telepathic attack on the mutants, which would have caused their powers to flare involuntarily, but the sequence was cut. The characters would later appear in X-Men: The Last Stand and X-Men Origins: Wolverine, respectively.
Refitted For Sequel: The bathroom set was originally built for a flashback scene Cyclops discovering his powers, that was left before being shot. Also, a scene similar to what they'd intended turns up in X-Men Origins: Wolverine.
Wag the Director: By shooting time for the film, Halle Berryhad more clout, and used it to give herself a bigger part (and more money) in the movie, and lo, here comes her conversations with Nightcrawler and strange use of powers against the missiles.