Revealing mistake: When the Red Queen scans the doctors in the lab, it displays "Dr. Anna Bolt." This is the name of the actress, not the character. (00:05:10)
Continuity mistake: When Rain tries the door on the train and fails, we see her face and her hair has 2 strands on one side of her face. Camera changes and now she's got 1 strand. (00:16:50)
Other mistake: In the beginning when Spence breaks the T-Virus vial, its fumes can be seen entering the ventilation system from holes on the wall. Shortly after though, when Dr. Blue, Dr. Brown and Dr. Green are trapped in the flooded room, the former of them claims it is "sealed." (00:03:05)
Audio problem: Near the middle. When Matt is searching through the office room where his sister Lisa worked, you can hear his shoes clicking as if he is on a hard surface floor, but the floor is covered in carpet throughout the office. (00:49:00)
Continuity mistake: When Alice and Matt run to meet up with Spencer, Kaplen, and Rain, Alice screams "Don't shoot!" and Spencer, Matt, and Alice try to close the door from the zombies. A zombie then grabs the inner part of Spencer's arm, then a shot moves showing the zombie holding onto Spencer's arm from the bottom, then back to the inner part. (00:55:45)
Audio problem: In one of the scenes right before the solider get killed by the lasers and the alarm is sounding, the commander says to everyone "Hold your positions, everyone stay calm" but his lips aren't moving. (00:31:20)
Continuity mistake: When the first laser passes through it hits the one guy in the wrist, however we see him on the floor missing half of his fingers and hand instead. (00:31:30)
Continuity mistake: In the laser corridor, the team leader is stood upright when the lights comes on, but as the camera changes to a front view, he is crouched. (00:30:10)
Suggested correction: It's easy to miss, but there is a quick insert-shot in-between these two shots that shows the team leader crouching down suddenly. (The camera is focused on the back of his head as he ducks down suddenly.) It can be seen in this video (https://www.youtube.com/watch?v=rOLe15-5Xhw&t=65s) around the 1-minute mark.
Continuity mistake: In the scene where Matt pulls Alice into the mansion at the beginning of the movie and the SWAT team comes through the windows, the main SWAT member pulls Alice aside and asks for her report. If you watch the scene Alice has one arm at her side and one across her chest. A split second later it shows her reflected in the eye lenses on the SWAT member's mask and Alice has her arms crossed in front of her. Another split second later they show Alice again and her arms are in the original position. (00:13:35)
