Continuity mistake: Hugo is running away from Zapan; after the sequence of Alita's busted pipe we see him jump over a parapet onto a street underneath, rolling just past an incoming utility vehicle. In the overhead shot he lands right in front of a group of people including a rather conspicuous man with a pink shirt, but in the following shot almost everyone in the street is gone. (01:34:40)
Continuity mistake: The position of Alita's hands on Hugo's face changes between shots a few times as she holds him in the church. (01:38:55 - 01:39:40)
Continuity mistake: The hair on the severed head under Alita's arm changes arrangement between shots. (01:41:00)
Continuity mistake: When Alita is playing the street version of motor ball she knocks over Tanji. In the next shot Tanji is following her in the pack as she scores, then the shot switches back to him on the ground.
Continuity mistake: In Alita's speech inside the Kansas bar, at first she does not have her Hunter Warrior ID in her hand. After the camera angle change it's in her left hand and then her hand is empty once more after the next camera angle change.
Continuity mistake: During the battle with Grewishka in the alley, the brute punches a hole in the asphalt and one into the tiles and concrete wall. However, after Alita axe kicks him from above and slides behind him to grab Ido's weapon, there are good views of the alley and no trace of the damage is present.