Continuity mistake: In the scene where Silk Spectre II visits Nite Owl II at his home, the small mole on her cheek disappears only to reappear again when they leave to visit Hollis Mason (Nite Owl I). It doesn't appear to be a staple of Spectre's makeup in any way and is instead permanent, as it was present when she left Dr. Manhattan to visit Nite Owl (directly before) and on the way to visit Hollis (directly after) as well as through the rest of the film.
Revealing mistake: In the scene in the Vietnamese bar, after the Comedian shoots his ex-lover and she falls to the floor, the camera shows a quick, panned-out shot of Dr. Manhattan and the woman on the floor. The bottom of her shirt is flipped up, revealing straps of the false pregnancy stomach she was wearing.
Revealing mistake: When Dr. Manhattan is interviewed on TV, his ex-girlfriend Janey makes a surprise appearance in the television studio and launches into emotional accusations. In one shot, we see both Janey shouting in the background and a live television monitor close-up of her face in the foreground. However, the TV monitor close-up shows Janey making completely different head movements than she is making in the background.
Continuity mistake: In "The Ultimate Cut" version of the film (and perhaps the original), Laurie and Dan have a discussion in a restaurant about the attack on Ozymandias. Outside, across the street we see people milling about. As the camera cuts between shots of both characters at the table, then close ups of Spectre, then of Night Owl, and back again, the positions of these people vary randomly, including a seated girl that appears instantly out of nowhere, then a man in a brown jacket walks over to join her, but instantly is seated next to her, then he's seen approaching and sitting down with her. (Timecode is for The Ultimate Cut). (01:41:10)
Revealing mistake: When Dr. Mahattan and Silk Spectre are on Mars and they are climbing upward in his gyrating clockwork structure, a shot from well above, behind and to the right of them contains some terrible CGI work of Silk Spectre walking in a completely unnatural, very mechanical way.
Factual error: In the scenes on Mars, two spherical moons can be seen in the background. However, in reality, the moons of Mars (Phobos & Deimos) are not spherical. Also they are so small, that they would only appear as moving dots in the night sky, not spheres like Earth's moon.
Other mistake: When Silk Spectre visits Night Owl she touches and notes the dusty aircraft under the canvas, as if it hasn't been used for a while. In fact at the start of the movie as the cops are investigating the Comedian crime scene, we see the aircraft hovering and listening in. Also, the aircraft has to go through a body of water each trip it makes, which would wash off any dust.
Visible crew/equipment: At the beginning of the movie when the Comedian is fighting with the mysterious masked man in his apartment and the first one is launched towards the table, the director Zack Snyder is hidden behind the kitchen counter and kneeling (this mistake is revealed by Snyder himself in the DVD extras).
Continuity mistake: When Kovacs is being interviewed before being given the Rorshach test, a pill bottle is shown on the table in front of him. The front label of the bottle faces Kovacs when first seen, but a moment later, with nobody touching it, the bottle has turned 90-degrees so that the label faces left of Kovacs, toward the camera. (Timecode is for The Ultimate Cut). (01:50:50)
Continuity mistake: When Dan returns home after talking to Mason, he finds Rorschach in his kitchen eating beans from a can. After he has finished eating, he throws the second can on the table where it lands next to another can. When he gets up, the two cans have moved significantly apart. (00:20:15)