Continuity mistake: In the end, when the President is visited by the X-Men, he receives a blue binder, which is laid in front of him on the table. When they have left, you see a shot including the President's desk, and you can see that the only thing he has on the table are some sheets of paper, stapled in the upper left corner, opened up. Then the shot changes to a close-up of the President, and then back again, and you see the blue binder in front of him, closed, and the papers have disappeared. (02:01:40)
Continuity mistake: When Viper confronts Shingen, she removes her left glove twice.
Continuity mistake: When Magneto lands the Golden Gate Bridge on the island, as it hits land it is still very light. When the Brotherhood start to walk toward the island, it cuts to a wide shot of them still walking on the bridge, and it's suddenly dark.
Continuity mistake: When Wolverine crashes into the tree knocked over by Sabertooth, notice that the entire front of the truck gets completely folded up and the windshield breaks into a thousand pieces. In the next frame, Wolverine gets thrown through the unbroken windshield and the front of the truck is practically undamaged... (00:18:05)
Continuity mistake: Near the start when Wade and Vanessa are discussing families, in most shots facing her she's got her thumb lying along his jawline, but in most shots facing him it's sticking up by his ear.
Continuity mistake: When Mystique is on the exercise table and Erik lifts the bar off her, her right leg changes from stretched out to bent from the different camera shots.
Continuity mistake: In the scene near the end where Ajax has a knife in the side of Deadpool's head and is punching him, later Deadpool pulls the knife out. In a follow up shot there is no hole in the mask where the knife was, but in a later shot the hole is there.
Continuity mistake: When Pierce first begins to interrogate Caliban in the safe house in Mexico, a large portion of Caliban's albino makeup is smudged below his nose, revealing the actor's natural skin in his first close-up of the scene; after switching to a close-up of Pierce, then back to Caliban, the smudge has been fixed.
Continuity mistake: Despite having the Phoenix power at the end of X-Men: Apocalypse, which manifests around her as a Phoenix firebird and she uses to defeat the titular villain, Jean Grey doesn't actually get merged with the entity until 9 years later in this movie.
Suggested correction: Jean used her full psychic powers in the previous film, not the Phoenix Force. Even without the Phoenix Force she was an incredibly powerful, Omega Level mutant.
The Phoenix firebird is literally shown to be emerging from Jean's body when she kills Apocalypse. She can't both have the Phoenix firebird already within her and then somehow also have it invade her body in this film. The mistake is valid, and I would argue it should be listed as a plot hole more than a continuity error.
Continuity mistake: In the scene where Kayla is dead and Logan walks to her, her mouth is open in one shot, but in the next shot when his hand is reaching for her eyes, her mouth is closed.
Continuity mistake: When Quicksilver duct tapes the guard in the elevator, the tape changes when Quicksilver and Magneto come back. For example, when they get back, the tape on the chin is now tucked under tape strips and there are more spaces seen.
Continuity mistake: During the last great battle with Apocalypse, Beast hurls an entire automobile at Storm, and she recoils in fright. Before the car crushes Storm, Psylocke slices the automobile in half, with the two halves separating by several feet (at least 10 feet) before the shot changes. But in the next shot, the two halves of the car crash down on either side of Storm, separated by only a couple of feet.