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. (00:05:25)
Continuity mistake: Near the end, at the chopper crash site, the Umbrella man lifts the corner of the sheet covering Alice's body. From the high zoomed out shot, the guard is facing the waterfall, while the next shot he is facing the body. (01:18:50)
Revealing mistake: Resident Evil Apocalypse was shot in Toronto and the filmmakers wanted to use the city surrounding the CN tower to be Raccoon City. They edited out the CN tower, however they missed a brief glimpse at it. It's shown really quickly in between when Angie's vehicle crashes and when it stops. (00:05:25)
Continuity mistake: Watch the scene where Alice almost pokes the scientist with the pen. In the close up shot of the guy's face, she almost poked him in his left eye. In the far shot, the pen is being pointed at his right eye. (01:23:30)
Continuity mistake: When Alice escapes from Nemesis falling into the garbage, she shows both hands with her fingers in good condition. Yet in the next shot, she has a very badly broken finger. (00:45:30)
Visible crew/equipment: A boom mic operator wearing a white shirt is seen reflected in the door that the female scientist opens, when the Umbrella personnel pick her up, as part of their extraction procedure. He is visible as the door is opening and very faintly when it is closed. (00:04:00)
Answer: The newspaper clippings we see in her apartment at the start refer to a 'mansion incident' - this in fact relates to the events of the first Resident Evil game, when Jill and other STARS members were trapped in a mansion overrun with the T-Virus. By the end of the game Jill knows exaclty what the T-Virus is and what its effects are.
Even though it mentions it in the newspaper clippings in the movie she wasn't even at the Mansion so therefore she wouldn't have known about the t-virus in the movie.
She was at the mansion prior to the events of Apocalypse, and one of the first ones to know about the virus before it hit Raccoon City.