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.
When Rogue is standing in line to receive 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.
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.
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.
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. When the pole is falling down, the lights are still on, even though the power line should be cut through. Then as Wolverine is fighting off more mutants, the light pole can be seen right behind him still up.
When Bobby takes Kitty skating on the pond, she has skates, and he creates 'ice' blades which are attached to his shoe by more ice. When their feet are then shown as they skate, his blades are shiny metal through the ice around the sole of his shoe.
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.
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.
Jean scratches her fingernails deep along Logan's upper arm while on the medical bed. The scratches reveal his muscles are covered with a silvery substance that looks to resemble adamantium. In all other movies in this series (and the source comics) it is made abundantly clear that only his bones are adamantium-covered.
When Magneto reveals the tattoo of the identification number he received in the concentration camp it appears on the inside of his left arm. As a male concentration camp prisoner, he would have received the tattoo on the outside of his arm. Only female concentration camp prisoners were tattooed on the inner arm.
In the prison chase, when Juggernaut charges towards Kitty Pryde, and then he smashes his head and lose consciousness because of the mutant cure, this shouldn't happen because Juggernaut isn't actually a mutant.
Alcatraz Island is a National Monument, and thus cannot be owned or altered by a private company like Worthington Labs. (This error is the result of combining two different plot elements from an earlier version of the script, see trivia.)
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 real bridge.
Magneto, in holding up the prison transport, causes the truck to separate from the trailer that holds the prisoners. Trailers of that type depend on air pressure to make its brakes work, air supplied by the truck's air compressor and supplied through airlines from the truck to the trailer. There were no airlines present; also no electrical line to operate the trailer's brake and signal lights.
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.
The Golden Gate bridge is a suspension bridge, and its structural integrity is dependent on its principle suspension cables (in tension) being held apart, and its towers (in compression) being held up. The anchors in the banks usually keep the suspension cables in tension, which is what usually supports the main span deck's own weight and loading weight. Normally, a catastrophic structural failure would happen when any of the points of attachment are detached. But when Magneto moves the bridge to the island, severing the suspension cables from their anchors and the towers from their foundations, he is clearly carrying the bridge's weight, making its designed structure irrelevant.
Throughout the movie, and especially with Wolverine fight sequences, there is not a drop of blood from any of the injuries the mutants and humans inflict on each other. Presumably this was done to keep the PG-13 rating and thus reach a greater audience.
When Magneto catches Wolverine in mid air and slams him on the ground, Wolverine has to look up, over his forehead to see Magneto. When Magneto says Wolverine never learns and Wolverine says he did, he is then looking down his chest at Magneto. (However, a part of the scene, where Magneto tortures Wolverine, was cut. During this Magneto turns Wolverine around. In the final version, we may assume this happens off-screen when we look at Magneto.)
In the final confrontation between Magneto's forces and the X-men, we see scores of angry mutants arrayed against a scant security force and only a handful of X-Men. Magneto has the ability to reduce the opposing "good" mutant numbers very easily yet doesn't do so. As Magneto's "pawns" are battling the defense force to get into the compound of the pharmaceutical company, Magneto himself stands on the remnants of the bridge watching the carnage. Though Magneto has the ability to control metal and manipulate magnetic fields, and Colossus, who in his mutant state is entirely metal, and Wolverine, who's body is laced with Adamantium structurally reinforcing his entire skeleton, are well within his power to control, he doesn't seize this opportunity to reduce the X-men forces by a full third.
When Magneto drops the bridge, Magneto then flies above the bridge to avoid the impact. The Impact is hard enough to crush several buildings on the island, but apparently none of the Brotherhood or the cars on the bridge seem to have been disturbed by falling 100 feet to the ground below.
The two opening scenes are established as taking place 20 and 10 years ago. Then after the opening credits, the rest of the film is said to be taking place in the not too distant future. While the exact date of this future is never exactly elaborated on, neither is when exactly the 20 and 10 years ago scenes take place from. Either from the then present day of 2006 (when the film was originally released) or the previously mentioned not too distant future.
When Wolverine thrusts his claws into the ceiling of Jean's house, once or twice you can clearly see the ceiling giving way to the pounding of his fists, revealing it is obviously some kind of foam instead of concrete or drywall.
The goof items below may give away important plot points.
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.
When Wolverine and Storm rush into the room to find Xavier's empty wheelchair after his death, Logan's claws are unsheathed. The next time it shows his hands, they are sheathed. Although it's possible he could have retracted them while off camera, the metal retracting sound would have been heard.
When Magneto relocates the Golden Gate Bridge, we assume that he, or Jean Grey are using their powers to hold the bridge up, since the structural integrity of the suspension bridge was destroyed when moved, and could not continue to stand on its own. However, at the very end of the Alcatraz battle scene, Magneto has been turned human, and Jean Grey has died, but the bridge remains upright and above water, despite no one holding it up.
After Magneto is "cured," the remaining soldiers fire their cure cartridges at Jean, which she quickly destroys, suggesting she might still be vulnerable to them. But even though Logan is unharmed by knives, kicks, and groin shots (as seen in the first X-men movie), he doesn't appreciate them. So Jean might only be stopping the needles because they annoy her - not because they necessarily could cure her.
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.
Magneto, who must be the target of a nation-, if not world-wide manhunt, sits calmly playing chess in the park without any disguise, in the city he was last seen in, in full view of several people. His face would be well known from his terrorist video, not to mention the inevitable "Have you seen this man?" notices which would have blanketed the nation following the Battle of Alcatraz.
Jean's destructive power kills people & obliterates all objects. Wolverine survives due to his healing power, and his pants stay on to keep the PG-13 rating. But all of his adamantium would have been disintegrated.