During the fight in the parking garage at the end of the film, the sound of one of the guards screaming comes after his head has been cut off and hence separated from the lungs, which would make a scream impossible.
Detective Sebastian fires a total of 7 rounds at the Antigen van in the parking garage - three at the driver, three at the front-left tire, then one after it passes him - without reloading, yet the Taurus Judge pistol he is using is designed to only hold 5 rounds in its cylinder. Later, after Sebastian has reloaded the pistol, he fires 8 rounds at Dr. Lane, again without reloading.
In the elevator scene with Selene and C4, she is seen planting the charges on the side of the elevator column against/with the doors. When the doors open, the charges are seen planted on the back opposite inside of the elevator cart.
When Det. Sebastian is watching the security videos, we see a shot of Dr. Lane taking Eve down a hallway, with the security camera preceding them down the hall (moving with them), rather than panning to follow them as would be expected from a fixed-position camera.
When watching the footage of the security camera on the security monitors in the 3D version, the Time and Date stamping on the footage is in 3D. If it were in real life this would all appear as a flat 2D image on the screen.