Plot contrivance: Simple question really: Why is Nightcrawler not killing the President faster? He teleport-punches his way to the oval office with incredible speed and yet decides to jump with the President on the resolute desk for some sweet Monica Lewinsky fantasy to slowly take his knife-out on him. Why? You are surrounded by dozens of soldiers that you incapacitated with your fists – surely a few of those soldiers' limbs are not broken and one of them will be able to aim his gun at you again as soon as you give him the chance. Oh one of them did? God – I am so sorprised I forgot how to spel.
Plot contrivance: Police officers are quick enough to shoot Wolverine straight-up in the head the micro-second he puts his claws back in his arms but when douchebag Pyro starts throwing individual fireballs to all officers surrounding him.....none of them do anything. They are all proud graduates of the Nightcrawler school of heavily-variable fight speed.
Plot contrivance: When Storm starts throwing hurricanes at military pilots to make them shit their cockpits – things don't go as planned and the Blackbird jet is hit by one missile and falls down...exactly a few feet away from Magneto and Mystique who just happened to be in that specific forest at this specific spot at this specific time with the only specific power that could stop the plane from crashing non-specifically to the ground.
Plot contrivance: If Jean Gray has the power to deflect an incoming river with one hand and lift the x-men jet with the other, why couldn't she do all of these things from inside the x-men jet's cockpit? I mean - there really wasn't any logical reason for her to go outside to use ranged powers.
Unaddressed Issue: At the end of the movie, the X-men go to meet the President to lessen the tensions between humans and mutants that started to go out of hand with the attempted murder of said president by bringing Nightcrawler with them, the attempted murderer, to stare and smile creepily in the background without giving any context or explanation as to why he tried to kill the president in the first place. Yes Xavier, your diplomacy skills are outstanding – you sound like the type of guy who would bring a KKK member to a Black Panther convention to ease tensions.
Unaddressed Issue: It's hard to believe Mystique could really have pretended to be Senator Kelly this whole time between X1 and the end of X2. Think about it: the fake Senator Kelly can only exist as long as everyone in his life still think he is alive and going on with his usual routine. He probably has a wife. Does Mystique fuck her every night? He probably has kids. Does Mystique play baseball with them on the weekends and cheer for their shitty skills at school events? He probably has important political meetings everyday? Does Mystique sit through all of them? This is some pretty intense and dedicated method acting: Mystique would make Daniel Day-Lewis jealous. What about the times where she has to be Mystique? She had to engineer a big plan to get Magneto out of his LEGO prison and eventually left with all of the X-Men to Canada to wreck some shit. What did she say to to the Senator's staff and family before she left? ''Ok I'm gonna sex-tourist the shit out of Canada! And I'm not a mutant obviously bye''.