- Miscellaneous: In the closing credits, the credit for Paint Foreman is misspelled as Paint Forman.
- Revealing mistakes: When Beast meets Leech, a close-up of Beast's face as he remarks on Leech's power reveals the net-like tape used to attach the blue fur to his face.
- Revealing mistakes: When Wolverine shows Jean Scott's glasses when he is trying to control her, a close-up of his hand reveals a small cut on one of his fingers. In the X-Men universe, Wolverine has healing powers that prevent him from having any cuts on his body for any significant length of time.
- Miscellaneous: While Jean Grey was tearing off Wolverine's skin, in the last and the biggest tear off, despite Wolverine has restored completely, when Jean Grey starts to tear off, the wounds previously occurred have healed in one frame, less than a millisecond.
- Continuity: Time of day during the final battle sequence. The first pan over the bridge from southeast looking north, is clearly midday as the shadow of the bridge is almost directly underneath it. When Magneto first walks onto the Golden Gate bridge it is close to sunset, and the shadowing is very inconsistent, sometimes sharp from direct sunlight, sometimes not. By the time they move the bridge and drops it onto the island, and lowers himself to the bridge, and all the mutants move forward, it is suddenly dark. In the DVD commentary, everyone acknowledges it, but says "Hopefully you're into the movie enough...” The whole battle is then shown as taking place in the dark.
- Revealing mistakes: When Wolverine leaves on the motorcycle from the school and goes to the woods looking for Jean, to Magneto's hide-out, he is wearing a brown leather jacket. But, once in the woods, he senses something, the camera pans down as he extends his claws. Although the DVD Commentary from the Writers & Director mention it and jokingly say "He has a mutant power here, the ability to lose his jacket. He has a jacket here, if you look at his sleeve... and now, no jacket." This is because right after that he is shown in nothing but the white wife-beater style t-shirt. But if you look at it in slow-motion, and see in subsequent shots, it is actually his watch. In some shots, his jacket hangs as low or lower than the sleeve and if he was wearing it, we would most likely have seen the front part of the jacket against his jeans in that shot.
- Continuity: In the woods at Magneto's hide-out, Wolverine is attacked by the mutant Spike. When he kills Spike, he has two spikes in his stomach on either side of his belly button. The wounds heal, and you see the holes in the wife-beater style t-shirt he is wearing, but in the rest of these scenes, the holes are gone.
- Continuity: When Dr. Kavita Rao prepares The Cure injection for Angel, at first, the needle clearly doesn't have the plastic protective cap on, then she takes it off in the next shot.
- Revealing mistakes: In the scenes of traffic on the Golden Gate Bridge, there are no yellow lane markers separating the northbound and southbound lanes. They are used to adjust the number of lanes in each direction, and they're always present on the bridge.
- Revealing mistakes: On several occasions, the line where Mystique's blue makeup ends around her mouth is easily visible.
- Audio/visual unsynchronized: When Scott rides to the lake, he is on a Harley-Davidson V-Rod, but the audio used for the engine noise is from a regular V-Twin Harley engine. The V-Rod's engine sounds more like a car than a typical Harley.
- Crew or equipment visible: Wires are visible during second "Fastball Special", where Colossus throws Wolverine towards Magneto.
- Continuity: When Professor Xavier and Magneto enter Jean Grey's old house and find her sitting on a chair, items in the room are levitated around her. When the items drop, the bookcase over her right shoulder hits the ground and all the books fall off, the lamp on top remains on. In a later shot the books are back in the book case and the lamp is on the floor.
- Miscellaneous: The word "too" is misspelled as "to" in the caption "The not to distant future". (Corrected on DVD version)
- Continuity: At the final battle, when the X-men are lined up, Wolverine is too far forward from the light pole to just swings back and cut (as he does) so it falls onto the attacking mutants, then as Wolverine is fighting off more mutants, the light pole can be seen right behind him still up.
- Revealing mistakes: When Magneto drops the bridge, he flies above it to avoid the impact, which is hard enough to crush several buildings on the island. But none of the Brotherhood or cars on the bridge seem to have been disturbed by falling 100 feet to the ground.
- Miscellaneous: At the end scene with Jean and Wolverine, there is a shot of him from behind, and his beard makeup is hanging slightly loose from his cheek.
- Continuity: After Magneto and his Brotherhood leave Jean's house after the fight, Wolverine and Storm are running to find Professor Xavier. In the shot just before they burst into the room he was in, Wolverine's claws are out. In the next shot he falls to his knees and his claws are in. There is no "SINKT!" metallic noise in between.
- Plot holes: When Wolverine arrives at Magneto's camp, he is attacked by Spike. It appears Spike is close behind due to the time it takes for him to throw the spike and when it is passing Wolverine. Wolverine is hit, and he pulls one out of his shoulder and appears to throw it into Spike's leg as Spike comes over the big felled tree. Another mutant comes over the tree after him, (with a gun, which was also an issue with the movie makers - why would mutants need guns?) and Wolverine fights with him and others, slashing his way through the forest, and then appears to arrive where Spike fell after being hit and appears to kill him - and that victim has the EXACT tattoos, clothing and hat of Spike, but appears to be wearing something from the elbow, to hand, and apparently had a shotgun. Then, Wolverine is being attacked again by Spike from a distance, but Spike had been following him closely earlier, so why would he be so far away? They get closer and closer and Wolverine kills him, and you don't see a spike in Spike's leg.
- Miscellaneous: Joël Einhorn's name is spelled as Joel ëinhorn in the end credits of the movie.
- Revealing mistakes: In the scene where Bobby takes Kitty skating in the fountain he uses his power to create blades on the bottom of his regular shoes, however, at certain points real blades are clearly visible underneath the ice he created.
- Continuity: When Magneto is stabbed by the "Cure" needles, the needles go from being in one direction with four, to three in another direction when it changes back to him.
- Continuity: When Magneto locates and rescues Mystique from the armored truck, Pyro reads Multiple Man's cell number as "41205." The actual cell number is 41209.
- Incorrectly regarded as goofs: When Juggernaut is inside of the building attempting to find Leech and destroy him, Kitty pulls him into the floor. Juggernaut's power is that when he has momentum nothing can stand in his way, yet he later destroys the floor holding him just by moving his arms up, he could never have gained momentum because he couldn't move his arms. However, Juggernaut's legs could have been dangling THROUGH the floor. If he wiggled them, that would be all the momentum he would need to break free.
- Factual errors: When Magneto raises the Golden Gate Bridge the towers are shown shattering as if constructed of concrete. The unpainted piers are concrete but the painted towers are in fact steel.
- Errors made by characters (possibly deliberate errors by the filmmakers): At the scene where Rogue is standing in line to recieve the 'cure', she looks over to read the picket signs that a group of mutants are holding up at the side. One of the signs, instead of reading 'say NO to the cure' clearly reads 'say to NO the cure'. At the top of the sign it says 'Say to' then 'NO' in large letters in the middle and 'the cure' at the bottom. Even reading it as "NO say to the cure" would be grammatically incorrect.
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- Factual errors: Juggernaut isn't a mutant, his powers come from a Gem. Therefore he shouldn't be affected by Leech.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Continuity: SPOILER: During the final battle, Beast and Wolverine spot unused 'cure' darts in a gun cartridge. At first there are four darts, then when they look again, there are three. Later when the darts are used against Magneto, there are four again.
- Continuity: SPOILER: After Wolverine stabs Jean, the scene shows that there are no cars missing on the bridge, but that isn't possible because Magneto threw dozens of them at the troops.
- Continuity: SPOILER: After Wolverine stabs Jean and the camera pans upwards to view the bridge, all of the cars have their headlights on, which is impossible because it was broad daylight when the owners abandoned them earlier.
- Incorrectly regarded as goofs: SPOILER: When Wolverine confronts Jean/Phoenix, her aura of strength destroys his clothing. Yet mysteriously, the "pants" region of his clothing is not destroyed. His entire suit is, presumably, the same material, so there is no reason one part of his clothing should remain while the other parts are destroyed. However, one must realize that the creators were shooting for a pg-13 movie, and therefore, Wolverine's pants must stay on.
- Plot holes: SPOILER: Magneto has led a mutant army in a "war" against humanity, personally killed countless people, and caused enormous property damage (not the least of which is uprooting the Golden Gate Bridge.) Yet at the end of the movie, after he has been defeated and "cured" of his mutant powers, we find him not back in prison, but playing chess in the park?
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