Revealing mistake: Nearly at the end, the scientists find Alice's body at the waterfall, one of the men lifts up the cloth to take a look at her face. Her face is badly burned on one side and she is pronounced dead. However, take a look at the left side of her neck, you can see her either gulp or take in a quick breath of air.
Visible crew/equipment: When the SUV is struck by the large truck and is pushed along while upside down, a camera mount can be spotted (helps if you use slow motion) and also, a tow truck can be seen actually pulling the SUV along the street.
Continuity mistake: When the girl is being chased by the zombies (just before we meet Carlos) the keypad for the door is right next to it. When she tries to enter the code, it is suddenly next to the small grey box.
Revealing mistake: At the beginning, when one of the black trucks has an accident, whatever is making the dramatic sparks is still running when that part of bodywork is off the ground.
Continuity mistake: Watch the left side of the mouth piece in Alice's mouth when she is in the tank at the end. In the shot up close to her left there is a plastic support going up, in the next shot of her right the support is pointing down, and after the scientist says "can you hear me?" and the shot is close to her, the support isn't even there.
Continuity mistake: After the gas explosion in the school, Angela reveals that Alice is infected. The woman cop asks "When were you gonna tell us that?" and the next shot shows Alice with burns/blood on her upper left arm. In the next shot as Alice goes to sit down, the severity and position of the burns/blood changes.
Plot hole: In the grave yard scene. It doesn't seem possible for a virus contracted through bodily fluids (blood, saliva) to get 6 feet down into sealed coffins, infect a half decomposed corpse filled to the eyeballs with formaldehyde and methanol (typically), and make a zombie that could break out of its casket and dig up six feet with naught but bare hands, a seemingly impossible task for even the fittest, healthiest and craziest human.
Plot hole: After Dr. Ashford was shot, he stayed down the whole time that Alice fought with Nemesis, they fought with Umbrella, and after they took off. How is that possible? According to all the other times they've been shot, and with the t-virus in their bloodstream, they reanimate almost ten minutes later -- not when the director wants.
Continuity mistake: Toward the end, Major Cain storms aboard the helicopter, shouting "Why haven't we taken off, yet?" The shot switches to LJ (Mike Epps)in one of the pilot's seats. As he says, "Because I normally drive Cadillacs" he punches out at Cain with his left hand. In the reaction shot, however, as Cain flies backward, the punching hand is LJ's right hand.
Continuity mistake: Nemesis has an ammunition counter for his Vulcan cannon. When Nemesis is shooting at Peyton on the bridge, his counter stops at 3997 rounds. Almost immediately he begins shooting at Jill, but now the counter reads 3688.
Revealing mistake: In the early aerial shots of Raccoon City, look to the left of the screen and you can see the CN Tower, a very recognizable landmark that is definitely in Toronto, not Raccoon City. This is due to the fact that film was shot in Canada.
Visible crew/equipment: In the scene where Nikolai is bitten and the horde bears down on the police and S.T.A.R.S., you can see some crew members and a floodlight.
Deliberate mistake: When Jill and Angela are in the cafeteria, and the first dog comes running at Jill, if you look closely, you can see Jill bounces back with impact before the dog actually hits her.
Deliberate mistake: In the scene where they're on the airplane, and the bomb has just been landed, there's a sharp instrument that's loose and starts going towards Angela, and Alice takes the fall. If you watch closely, the sharp instrument is aiming towards Alice's right shoulder, but ends up meeting her stomach.
Continuity mistake: In the church scene, Alice blows up her motorcycle with two shots of her Colt .45's. During the shot of her back, she already starts with holstering her guns, her arms are already halfway there when the shot cuts. Then, there is a quick shot of the explosion, and in the next shot her arms are straight again, in the position where they were when she took a shot at her bike. There is no reason or time enough to do that.
Continuity mistake: A zombie hits its head on a tombstone, which falls over. In the next shot, it's upright again.