As the swat team makes its way through the flooded labs they stop and in a group shot Spense can be seen mouthing the words "What happened here?" but there is no sound. In the next shot he says it again this time with audio.
When she enters the Hive, Alice, straight from her shower, has on no makeup. As she travels through the hive, however, her makeup changes from scene to scene. This is especially obvious when her lipstick shade changes drastically several times.
When "One" is being killed by the laser grid he should have fallen into pieces (cubes) but in a later shot when the rest of the team enters the area you only see the bodies of the soldiers but no scattered pieces of "One".
In the Red Queen chamber, One's character is clearly only a few feet from the door. As the laser returns to kill him, you can see through his first person view that there are no bodies and no equipment in the corridor.
Near the end of the movie, when Alice is talking to Rain on the train, in the background, you can see Matt go from moving around to standing still with his hands on the sides of the doorway between shots.
At one point, the lights in all the chambers in the dining room change from the green "stable environment" to the red "unstable environment" and stay that way for some time. But during the gunfight one tank gets shot and a close-up of it shows the light change from green to red again (although, possibly they changed back from red to green when the power came back on).
In the utility tunnel, when the zombies reach through the mesh, the wires are not bent or broken to allow their arms through. When Alice's face is seen from the zombies' point of view through the mesh, you can see a neatly cut square hole.
When Alice tries to retrieve the anti-virus box on the train platform, there is an observation camera shot from above with filming equipment (probably a microphone) visible at the bottom of the screen.
When One and three other team members are trapped in the Laser hallway, the medic gets her head cut off, and when the camera jumps to Alice pounding on the door screaming to open it, you can clearly see someone standing (head still intact), facing away from the camera in the window on the door, yet all the team members are lying on the ground.
When Matt kneels down to examine the blood of the undead Hive worker, he claims that blood only coagulates when you're dead. In truth, coagulation is simply the process of blood clotting around a damaged vessel wall, which indeed happens in living beings. On the contrary, in death, blood doesn't coagulate, but separates, causing livor mortis.
The Red Queen tells the survivors that the human body remains active even during death, producing new cells such as hair and nails. This is a common misconception, as the skin of a dead body gradually pulls away from hair and nails as the body dehydrates, giving the appearance of the hair and nails growing. No new cells can be produced by a dead organism. Furthermore, neither hair nor nails are made up of cells; they are made primarily of a protein called keratin from dead epidermal cells.
When Spence listens in on Alice's conversation, he is using a standard shotgun microphone on a zeppelin shock mount. This is a location sound piece of equipment for film work. Although a shotgun mic does have a decent reach, it is not a suitable (telescopic) microphone for spy work.
In one of the early scenes, where a group of people is trapped in an elevator and they listen to another elevator dropping, there's a factual mistake in the shot portraying the fall of the second elevator. As the second elevator is falling, we can clearly see the counterweight rising, but when the elevator hits the ground and the wires snap, they just hang there. In a real life situation, the counterweight would've gone slamming towards the ground, pulling the wires along with it.
At the beginning of the movie, where the vial containing the virus is dropped, the fumes escape into the building through an air duct. This is not plausible, as any clean room that requires people to work in safety suits would be sealed, and therefore not have air vents.
When the Umbrella special ops team debarks from the train, and the Red Queen's camera is tracking them, we see it highlight each of the team members in turn, and a small image of their face is shown, under which appears a spinning graphic of the gun they are carrying. However, every member is shown to carry the same weapon: a Heckler-Koch MP5, though it is clear that JD carries a modified H&K G36, and that the sergeant (who's weapon is clearly shown on the security camera) is carrying a modified Enfield L85-A1.
When the zombie lab tech attacks Spence in the water filled laboratory, he fires several rounds from a large caliber semi-automatic handgun without a silencer. The weapon appears to be a .45-caliber Colt 1911. It should make a resounding "boom" when fired, especially in that small space. Although there is a subdued "boom," the shots sound much more like those of silenced weapon.