Continuity mistake: When Sam is in his bedroom, after he finds the Cube sliver it falls and dramatically burns a hole through the floor into the kitchen. But Sam's bedroom is over the living room (there is nothing on the ground floor below Sam's elevated bathroom, and in the first movie Jazz hides in this open space), and the kitchen is actually located between the den and dining room, at the other end of the house. If they were to follow the actual floor plan of the house, the Cube sliver would have landed in the area of the piano in the living room, but where would the fun have been in that? (00:12:30)
Continuity mistake: In the scene where Parker is shown playing golf on the indoor golf course in RDA, the first time he hits the ball, there are two other balls lying on the course side by side. In the next shot, two are distant apart and in the shot after that, they are in their original position. (00:12:15)
Continuity mistake: In the scene where Blair escapes with Marcus and Barnes launches an explosive into the tunnel, Marcus hops onto Blair to save her from the scorching flames. After the fire, Marcus' coat would have been burnt to a crisp, his hair singed off and the skin on his back fried. More evidence pointing to this was that his coat was merely one previously worn by a Resistance fighter, not special in any way, and he has regular skin and hair. (01:06:50)
Continuity mistake: After the car chase, the front plate of the taxi is hanging on one side. Moments later, while driving the cab and fighting the other "alien," the plate on the taxi is in a different position (semi-fixed). (00:46:00)
Continuity mistake: During the sheriff interview scene with Abbey, the time is listed as 3:45am, but later in the scene, the clock reads 2:15am.
Continuity mistake: It's shown in many scenes that the robot Gallaxar sends isn't particularly quick moving when it walks. But when it's chasing Ginormica around the city, even though Ginormica is sprinting away, it can catch her far more quickly than its speed would allow. It doesn't suddenly speed up - in the shots when the camera focuses on the robot again, you can still see it moving slowly.
Continuity mistake: At the end of the film when Kirk is being awarded his medal, behind the Federation Counsel you can see 3 flags in the background- the center flag is the California state flag. After Kirk shakes Pike's hand, and the camera pans up and back, the California flag is hanging significantly different so that it is no longer recognizable, seeming almost blank white. As the ceremony is indoors and all attending are standing motionless, this flag should not have moved. (01:56:25)
Continuity mistake: When 9 meets 3 and 4, they open his zipper. During this scene, several close-ups show 9 with the zipper closed and open again without anyone closing or opening it.
Continuity mistake: When Ana returns home to her husband, they converse outside the house. He asks her how it was in Monte Carlo. As he asks her this, she is entering the front door and he is about 8 feet behind, following her. The next shot shows them both in the house, and they are very close together when she answers that she didn't get what she want. (00:25:15)
Continuity mistake: Near the end of the movie, when Christopher is pulled from the armored car and questioned about his plan, his arms are tied behind his back. A little later, when he is kneeling and the order is given to kill him, his arms are still tied. When Dinkus returns, Christopher is still on his knees, even after a soldier to his left explodes. A moment later, Dinkus arrives in front of him and Christopher is still on his knees, but now his arms are free.
Continuity mistake: When Sam 2 places Sam 1's helmet on his head before placing him back into the damaged rover, the faceplate is still blood-spattered and dirt-smeared, obscuring Sam 1's face. However, when Sam 1 is settled into the seat in the rover, the faceplate is very clean and his face is visible.
Continuity mistake: The aircraft used to deliver the pheromone lure to the creatures starts out as a F-15, then after a few shots it becomes a F-18 then back to an F-15 for a few more shots, then back to a F-18 and is finally a F-22 when knocked out of the sky by the giant octopus. (00:44:00 - 00:45:30)