- In the first shot of the Oval Office, the sculpture in the foreground is a copy of Frederic Remington's "Coming Through the Rye".
- The Danger Room, the area where the X-Men train and hone their powers, was going to be included in this film. Bryan Singer had wanted it to appear in the first film, but due to budget cuts, the idea had to be scrapped. It was then worked into the story for this film, to take place when Wolverine is left to watch after the students in the mansion. He decides to do a workout in the Danger Room, which was going to segue into the scene of him lying down and having a vision of Stryker and his Weapon X procedure. The Danger Room was going to be a cylindrical-shaped room, with different sections of the floor raising and lowering at dangerous speeds, as well as holographic projectiles, etc. The earliest teaser trailer for the film gave a sneak peak at how the Danger Room was going to look, but shortly after this teaser was released, Fox cut Singer's budget down from $125 million to $110 million, forcing Singer to once again cut the Danger Room from the film. There is still a small reference to the Danger Room remaining in the film: when Stryker first enters the X-Mansion subbasement, directly opposite from the elevator is a door with a small label on it, which, according to Singer's DVD commentary track, identifies the door as the entrance to the Danger Room.
- Movie Goof (plot holes): When Stryker visits Magneto to interrogate him, he enters Magneto's cell while still wearing his glasses, which have metal legs. The scanning process should have caught that on his way in; if it hadn't, Magneto should be able to manipulate them and use them to escape. It was shown in the first movie that Magneto can manipulate even non-ferrous metals, so he should have been able to affect Stryker's glasses.
- Movie Goof (revealing mistake): Nightcrawler is visible in the shadows behind the children before he and Storm arrive at the cell.
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