When Six is hanging over the well, he knocks off his left shoe to check the depth of the well. After he is rescued, he and Violet walk through a door and he has his left shoe on.
When Violet jumps off the building with the package, she cracks the ground, from the aerial view when she walks away from it, the ground is undamaged.
When Violet gives Six her credit card so that he may buy something to eat, he is wearing a pendent around his neck and his smock is without the three black patches that Violet removed shortly after rescuing Six. When Nerva pulls Six up the manhole, Six is not wearing the pendent and the three patches are missing from his smock. However, as Six struggles with Nerva outside the gate to the cemetery, the patches are visible and the pendent is missing. When Six is hanging over the well, the pendent is around his neck again and the patches are no longer on his smock.
After Violet and Six get off the train, Six pauses and looks up at a large building, and Violet talks to him. In one of the shots, his scar moves from above his left eye to above his right eye.
In the 88-minute cut, it seems (according to the flashback) that Violet's husband was killed in the raid where she was infected with the virus. This may have been the result of bad editing; the studio may have also intended the change since they released their edited version. This directly contradicts the scene from the unrated DVD in which Violet discovers that her husband has remarried, believing her to be dead.
When Six is balancing on the railing on the top of the skyscraper, the safety harness underneath his shirt is visible.
When Nerva and his gang meet up with Daxus, Daxus accidentally calls Nerva by his real name- "Sebastien."
When Violet is on the motorcycle on the roof and is about to speed towards and jump through the helicopter, she spins the back tire and then pops the clutch and takes off. If she was holding in the clutch, the back tire would not be spinning.
Six's left eyebrow has a sliced separation in it. In the movie, this jumps from left to right a number of times, showing that the film is flipped in spots.
When Violet enters the library with the lone guard standing there, the shots alternate between a close-up of her face and her looking around the room. The bangs in her hair switch from left to right indicating the shot got flipped during editing.
When Violet leaves with Six she says "Don't over-think it, just turns out I was right" but her mouth clearly says something else.
When Violet shows up at the cemetery she talks for a few seconds with the hemophage that has dreadlocks. At one point, before they fight, his mouth is moving as if to say something but there is no dialog heard at this point.
When Violet is talking to Garth on her headset, she says "I crossed Nerva" and then her mouth continues to move for a few more seconds, but nothing is heard.
In the cemetery, Nerva tells Violet "gunfire will attract the human security teams" convincing her to drop her pistols. Moments before, one of the hemophage henchmen fired several rounds at Violet on the street outside, with no security response.