When Spence enters the secured room where the T-Virus was stored he suddenly experiences the flashback of him stealing it. This is remarkably similar to what happens to Ark Thompson in the game 'Resident Evil: Survivor'. He wakes up with no memory of who he is, fights his way into a lab complex and suddenly remembers everything before encountering a Virus experiment gone wrong. I don't think it was done intentionally but it's an interesting game reference nonetheless. See more...
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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.
Continuity: 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.
Revealing: 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: Spence and Alice are charged with making sure no one without proper clearance gets into the Hive. Why then does Spence have the clearance to get into the Hive's most secret and secure area, the T-virus storage? Does a bank guard at the door have the combination to the vault? Can the guard in the entrance of a missile silo launch a missile? Of course not. There is no reason for him to have access that deep into the Hive. And while he may have bought the codes to get in, why does no one in the most secure facility in the world give him a second glance? Did he buy off every security guard and Red Queen as well?
Continuity: On the train, just after Spence falls in, Alice takes off her wedding ring and sees on the inside: Property of Umbrella Corporation. However, after she finishes off Spence, she drops the ring next to him, and in that shot, the inside is clean; or at least the half we can see when it lies still. Such a long line would take up a lot of room on such a small ring in that size text.
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.