Revealing mistake: After the first bus explosion when Jack answers the phone, he looks at his watch, which shows 8:05 a.m. If you look closely the watch is on alarm, not regular time.
Continuity mistake: After Gerry gets smacked in the face by the 'broken' suspender clasp, we see the silver clasp land under the dresser. Yet, when he's moaning and lifting his leg to get onto the bed, we can actually see the clasp still intact on the front suspender that came loose, which is dangling right behind him (just look between his legs). Of course, in the next shot, that clasp is gone. Since the silver clasp is one of the plot points, this is bizarre to say the least.
Continuity mistake: When John and Catherine are in the hangar at the runway, the Cessna's tail number is N3035C. When the plane is shown in the air, the number is N3973F. When they land, the tail number has changed back to N3035C.
Continuity mistake: In the bedroom scene the girl is holding a clear cup full of beer. The camera goes off her and when it comes back she is holding a blue cup. The camera goes back off her then on her and the cup is clear again.
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?
Factual error: The plane that returns some of the troops to the USA in the last scene is displaying the registration VH-HID - this is a current Australian aviation registration number, not a US plane.
Factual error: The detective played by Rory Kinnear is shown in 1951 typing a request for Alan Turing's military records. He changes a name with correcting fluid - unknown in the UK in 1951.
Other mistake: When Steven Hawking's life is played backwards and then rewinds at the end of the film, the sequence of his sudden illness at the concert and subsequent operation at the hospital are the wrong way round. It should show him having the operation, then winding back to his collapse at the concert, but the two events are in the wrong reverse order.
Continuity mistake: When they come over the mountain, Moses looks out at the Red Sea and sees nothing on the horizon. When they get across, they can see the mountains where they crossed very easily - the area on other side has mountains similar to the ones they crossed, which should have been visible when first approaching.