(at around 1h 15 mins) 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.
(at around 45 mins) 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 around 1h 20 mins) 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.
It is shown in X2: X-Men United (2003) that Colossus turns into steel, except for his hair, but in this movie it's shown that his entire body including hair turns into steel.
(at around 53 mins) 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.
(at around 1h 16 mins) The Golden Gate Bridge is 1,280 meters from pylon to pylon. Alcatraz is 2,400 meters from land, yet when Magneto moves the Golden Gate Bridge, it seems to connect Alcatraz with San Francisco.
(at around 40 mins) 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.
(at around 19 mins) 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.
(at around 1h 15 mins) 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.
(at around 1h 13 mins) 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.
(at around 1h 15 mins) 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.
Nobody brings up the idea of injecting Phoenix with the cure, which would be a way to stop her without killing her.
However the Phoenix Force, is not a mutant power. It is shallowly implied in this film that it is an evolution of Jean Grey's power; but the Phoenix Power has always come an outside influence.
(at around 1h 22 mins) 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.
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.
(at around 1h 24 mins) 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. In the comics continuity, yes, but the film version is portrayed as a mutant. There's no indication that the Gem of Cyttorak, the Juggernaut's power source in the comics, exists in the movie.
On several occasions, the line where Mystique's blue makeup ends around her mouth is easily visible.
(at around 22 mins) 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.
(at around 1h 30 mins) In the final conflict between Jean and Wolverine, there is a shot of him from behind, and his beard makeup is hanging slightly loose from his cheek.
In the end scene, the three graves are shown with grass growing uniformly over them. If the graves had been freshly dug, one would assume there would be no grass, or at least a visible border to the grave.
(at around 24 mins) At the edge of Alkali lake, Cyclops shields his eyes from light as Jean ascends from the waters. The shadow intended to be cast on his eyes by use of his hand is instead cast beneath them.
(at around 23 mins) 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.
(at around 1h 16 mins) 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.
In the final confrontation between Magneto's forces and the X-men, scores of angry mutants are seen 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, 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, whose 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.
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.
Magneto explicitly tells Juggernaut to keep everyone out of Jean's house, yet as he fights Wolverine, Juggernaut throws Logan directly into the house.
(at around 35 mins) When Magneto hijacks the prison transport, Pyro reads Multiple Man's cell number as "41205" but the number is visible as 41209.
Juggernaut was not known to be a mutant in some of the comics. The Gem's mystical power transformed Marko into Cyttorak's avatar on Earth, the Juggernaut.