At the beginning of the movie, Spence is wearing a leather jacket, which he gives to Alice. As the movie progresses, the jacket does not look big on Alice and even looks like a ladies' size.
It seems that no one's handwriting matches that on the note, not even the handwriting of the note's original author (as seen in flashback).
(at around 10 mins) The note written to Alice by Spence is seen twice during the movie, however when he is seen writing the note (at around 1h 12 mins) the handwriting is completely different to the writing on the note seen at the beginning.
When she enters the Hive, Alice, straight from her shower, wears 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.
Matt is supposed to be in handcuffs for at least the first 40 minutes of the movie, between one shot it shows him walking swinging his arms without cuffs on.
(at around 58 mins) 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.
(at around 2 mins) 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.
(at around 40 mins) 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.
(at around 32 mins) The first and last victim of the slicing laser would have immediately fallen to the floor as the laser passed through their spinal cords, as the muscles required to stand would immediately cease to function with no nerve impulses going to them.
(at around 5 mins) A group of people are trapped in an elevator and they listen to another elevator dropping. As it falls, 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 around 5 mins) When the lab at the beginning of the movie is filling with water, the camera scans the female scientist and her name shows up as Dr. Anna Bolt. Anna Bolt is the actress' name while her character is Dr. Green.
At the beginning of the film, when the virus vials are being loaded to the metal briefcase, the operator of the robotic arm drops a vial, and reaches for another one when its out of the camera's view , but it can be seen in the reflection in the window.
(at around 8 mins) At the beginning of the movie, you can see the floor outside the elevator bending under the woman's weight as she tries to escape the elevator.
(at around 49 mins) The zombie in the kennel, after being kicked back (as well as before that) can be seen breathing.
After Matt is saved by Alice, one zombie falls after soldier stops shooting.
When the tactical team first enters the house above the Hive, they are all wearing gas masks, however, none of them has filters attached and would, therefore, be useless.
(at around 24 mins) As the swat team makes its way through the flooded labs they stop and in a group shot Spence 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.
(at around 20 mins) When Kaplan says, "accessing schematics of the hive", it can clearly be seen for a split second that his mouth isn't moving to the dialogue.
(at around 50 mins) When Alice runs along the kennel wall to leap up and kick the last dog, you can clearly see a black wiring harness used for the stunt, under her jacket and dress.
When they are first entering the hive and the captain is speaking to Alice, a sound microphone is clearly visible at the top of the screen.
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.
The sanitation team are aware that the Red Queen is a sophisticated artificial intelligence that "went homicidal". They would be under orders, and would have explained the orders to the "civilians" they found, to not speak about their plans concerning the Red Queen until the Red Queen was not capable of defending herself with the level of force seen in the corridor sequence.
It's implied that the Red Queen controls the laser room hallway, which means she killed the first four commandos. If the Red Queen was trying to convince everyone that they can't cut the power lest the virus escape, a simple solution would be to let them enter her chamber, and she would tell them to go back to the flooded lab to see the drowned zombie, proving her claims. By killing the commandos immediately, they will no longer trust her. This makes the Red Queen, who is supposed to be an intelligent supercomputer, look very foolish.