Watch Milla Jojovich's hair during the scene when they are held at gunpoint by Spence. Her hair moves from shot to shot. For the most obvious, watch right after Spence shoots the zombie. See more...
A subtle reference to the games: The name on the front of the transit train is 'Alexia'. This could be a reference to Alexia Ashford, an Umbrella researcher who appeared in 'Resident Evil: Code Veronica'. I'm also fairly certain the names 'Red Queen' and 'Hive' are attributed to Alexia's fanatical obsession with ants and the fact that the T-Virus, in the games, was supposedly discovered in an ant corpse. See more...
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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.
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