Factual error: When the USAF car arrives to speak to O'Neil, the car has a GSA (Government Services Administration) license plate on the front. As you see the door open, the printing states an Air Force Registration Number, meaning this vehicle does not require a GSA tag and should have a license plate with the letters USAF.
Continuity mistake: RA continues to wear the necklace at the end of the movie when it was taken from him by Daniel before he left the spaceship via the transporter.
Other mistake: When one of Jackson's crew raises his 35mm camera and takes a picture, there's no lens on the camera.
Other mistake: When the ship lands atop the pyramid and begins to retract and open the topmost sections of the pyramid retract into the lower parts however the upper parts are too long to fit into them. In the next sequence we see the ship and the upper parts are nowhere to be seen.
Suggested correction: Perhaps the parts fold further in on themselves. Like a retractable ladder.