Other mistake: Near the beginning of the movie, Milla Jovovich reads a note that has been left on the desk. She didn't write it, as they demonstrate in the film. However, when they do show the person who wrote the note composing it, the handwriting is different from that in the note from the earlier scene.
Continuity mistake: Near the end, when Alice, Rain and Matt are talking to the "Red Queen" in the virus lab, there is a wall-mounted LG Flatron TFT display where the Red Queen shows surveillance footage, etc. One can see an inventory type barcode label in the bottom centre of the screen. The camera cuts away briefly, and when the camera shows the display again, the barcode label is gone and the LG logo is in its place.
Continuity mistake: The way the T-Virus capsule hits the ground is the same each time they show it, however when it's on the ground and motionless, the position is changes. During the flash back at the end that Spencer is having, the capsule is all over the place. However at the beginning, the capsule is just in a little straight pile on the floor.
Continuity mistake: When Matt is at Lisa's desk he looks through some papers, he is looking at a paper which has black squares on it. Then he puts the paper down and looks at another paper. When it cuts to him noticing Lisa approaching he is now holding the paper with the black squares again.
Revealing mistake: In the scene where Milla Jovovich shoots the dogs with the 9mm Beretta she obtained from the dead security guard, a closeup of the gun is shown. Watch the cycling of the slide and you will notice that the ends of the bullets are crimped, indicating the use of blanks.