Plot hole: After Dr. Ashford was shot, he stayed down the whole time that Alice fought with Nemesis, they fought with Umbrella, and after they took off. How is that possible? According to all the other times they've been shot, and with the t-virus in their bloodstream, they reanimate almost ten minutes later -- not when the director wants.
Plot hole: In the school building, Nikolai is mauled by the police dogs that were affected by the T-virus. We see him lying dead on the ground several minutes after the attack and he still hasn't become a zombie. However, when someone dies they almost instantly come back.