Corrected entry: The T-Virus escapes through the air vent and spreads throughout the entire building, so the air vents must go all over. Later water floods the labs, all of which have air vents, so the rooms shouldn't have filled with water, it should have poured through the air vents and spread throughout the building.
Corrected entry: The T-Virus is being developed as a biological weapon. The virus doesn't kick into effect unless someone is wounded or dead, and even then it resurrects them as the "living dead". Those that are living and are exposed to the virus without treatment are perfectly fine for a good length of time before mutation into the "Nemesis", allowing ample time for retaliation. Not the best weapon around.
Corrected entry: In the scene by the elevator at the start where the woman gets stuck in the lift doors and gets decapitated you clearly can see the skyline of the city filled with other skyscrapers and it is broad daylight outside the window, yet the Hive is located underground.