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 of the film, on the train ride out of the Hive, Rain is quite close to becoming undead. When she speaks, we notice her teeth are still "movie-star white". However, a few shots later, when she becomes a zombie, she sort of hisses where you can see it has taken what couldn't have been more than a few mere minutes for her teeth to become brown and discolored.
Plot hole: Red Queen is extremely conveniently programmed for the plot of the movie. 1. Rather than seal off rooms in a place she has TOTAL control of, (that by the way is designed to be isolated in sections for this very reason), she lets the infection spread to everybody in the Hive. She could have easily contained it in a small section of the facility. This is standard procedure in ANY biowarfare lab, there is no way she wouldn't be programmed to do it. 2. Rather than let everyone know the virus is loose, she just starts killing everyone. She had counter-virus available, why not let everyone know that they are locked in with the virus, but help is coming? The infected personnel would be hit with it only minutes after infection. If it didn't work and they died, they are still locked in. 3. Instead of calling Umbrella and telling them the virus is loose, she clams up and just slaughters everyone. This guarantees that Umbrella will ignore anything she has to say, and breach the Hive with a response team and release the virus, the very thing she is programmed to prevent. 4. When Kaplan is disabling her, she keeps telling him that it's a bad idea, but doesn't bother to let him know that shutting her down will release hordes of flesh-eating killers. 5. She just assumes that Spence, no matter how he got in to the T-virus storage has clearance to stuff it all in a duffel bag and walk out with it. She could have locked him in and double-checked with Umbrella. 6. The entire reason for her existence is to prevent the virus from escaping, while almost every decision she makes greatly increases the chances it will get out of the Hive. This is way beyond bad programming - this is highly advanced AI doing the exact opposite of what she's designed for.
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Revealing mistake: When the group is being attacked in dining hall B, they are trying to get the doors open. J.D. is firing at two zombies and turns away to open the doors himself because Kaplan keeps forgetting the code. If you look closely, one of the zombies reacts a second late from being shot down.
Revealing mistake: On the DVD commentary, the director says that he only had a handful of the experiment cubes in Dining Hall B and used cardboard cutouts for all the others. This is most obvious when Rain is walking through the hall alone to check on the first zombie: the cubes in the distance don't match the rigid rows of the ones in the foreground.
Plot hole: Why didn't Umbrella's higher ups just ask Red Queen what happened before sending in an assault team? She could have told them the T-virus was released and the hive would have stayed sealed. Instead, they just assumed she was nuts and sent in people to shut her down! Had even one of them said, "What happened?", the zombies would have never been released - it's a plot hammer that contradicts the whole point of having an AI run the hive. There should have been a line that said something like "All attempts to communicate with Red Queen so far have failed. The whole point of an AI that has the capability to seal the Hive is to keep the virus from escaping! Her refusal to communcate guarantees that the hive will be breached by a team that is investigating.
Add timeGrumpy Scot
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: When Alice escapes the first zombie dog and locks herself in the room, a zombie approaches her and she kicks him down. When the zombie falls you can see his tie is partially outside of his suit. When it cuts to Alice reaching for his gun, the tie is tucked inside his suit.