Meredith Vickers: Good morning. I am Meredith Vickers, and it is my job to make sure you do yours.
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Continuity: When the Prometheus collides with the departing spaceship, the close up of the impact shows devastating damage which results in a massive explosion and fireball as seen from the ground. However as the spaceship falls to earth there is no sign of any damage from the collision or explosion in the area where the Prometheus hit the ship.
Continuity: When Vickers enters Peter Weyland's room to speak to him just before he embarks to see the engineer, her hands are clasped behind her. They remain that way in each shot where she is seen from behind. But every time the camera angle changes and we see Vickers from the front, her hands are suddenly clasped in front of her. This switching occurs repeatedly throughout the scene.
Continuity: Prometheus is flown into the alien spacecraft, presumably to disable it from flying. However, after the alien craft has crashed and rolled over Meredith Vickers, the ship is facing face down on the planet, giving us a full shot of the back of the ship. There is no damage to the back of the bulkhead whatsoever, even after the bright explosion in the atmosphere.
Factual error: At the start of the film, the alien drinks some substance and starts to disintegrate into the water. You can see his DNA (double helix formation) floating in the water. This is impossible because DNA is in molecular level. You should only see his DNA floating amongst H2O molecules. Moreover - the alien substance appear to melt the DNA into black strands- impossible for similar reasons of molecular level of the structure.
Continuity: During the final scenes, after the ships have collided and crashed to the surface, Elizabeth finds David's detached head inside the alien ship. She then takes the head with her to a ledge where she is about to lower David's body to the ground. In both places, David's hair keeps changing between shots: messy/neat/very messy, with no logic whatsoever.