At one point Mia is supposedly carrying a video camera; however, her shadow does not show this.
Margaret appears out of nowhere when you attempt to scavenge a part of the serum. Even if you look to where she would pop out from, it's just a desk against a wall.
Several files in the game state that it takes 3 days minimum for the Mold infection to take complete control of it's victims, but the Daughters DLC show the Bakers fell to this in less than an hour.
If a gun is fired in a cutscene, it dies the deplete the amount of ammunition available to the Player.
If you kill Mia in another area that isn't the largest space in the attic, you'll both suddenly be teleported there for Jack's introduction.
In the 'Happy Birthday!!' video, the first-person view is that of a man who is initially tied up, with the camera following his head movements. The tape is in S-VHS format, which would make the camera too bulky and awkward to mount on a man's head.
The shadows cast by weapons in the light of the flashlight beam are not how shadows would appear.
The firing caps on spent grenade cartridges show no signs of having been struck by the firing pin.
Doors can open both ways.
In spite of having been missing for 2 years, the ship still has its lights on.
Margaret screams for Ethan to stay out in a rage, but her face is a malicious smile.
Zoe tells Ethan to 'Use the serum on him' when he is attacked by Jack and he does so. Afterwards Zoe is freaked out by the idea that there is only one serum left, even though she knew that there were only two to begin with.