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.
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 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.
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. The previous movies and the comics all state that only his bones are adamantium-covered.
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.
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 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.
The Golden Gate bridge is a suspension bridge, and its structural integrity is dependent on its principle suspension cables (in tension) being anchored on land on either side, and its towers (in compression) being solidly rooted on the bay floor. The anchors ensure the suspension cables are held in tension, without which the main span deck's self weight and loading weight would cause a catastrophic structural failure - which singularly fails to happen when Magneto moves the bridge to the island, severing the suspension cables from their anchors and the towers from their foundations.
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.
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.
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-mens 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.
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.
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.
When Magneto rescues Mystique, he 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.
(at around 1 min) When Jean takes off Scott's glasses and asks him to open his eyes, her own eyes have changed from the previous movies; they are black. But in several shots it's clear she's wearing contacts; you can see the edges on her left eye.
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.
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?
One can assume that Magneto simply escaped in the panic and confusion during the Dark Phoenix rampage. It is very unlikely that Magneto was simply given a full pardon due to having lost his mutant abilities. However this still leaves the question of how he could be safe to sit in a public place without any disguise, considering that he remains in the city he was last seen in, and his face would be well known from his terrorist video.
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.