Plot hole: Why does Umbrella know that Red Queen killed everyone, but not that the virus is loose? Is there no way to see into or receive data from the Hive other than Red Queen? Does every communication in or out have to be approved through her? And even if she is the sole conduit for information into and out of the Hive, her primary purpose for existing is to keep the T-virus from escaping. Umbrella THINKS that Red Queen has malfunctioned. BUT, she is working perfectly! So suppressing info that the T-virus is loose in the Hive would contradict her core programming. So why doesn't Umbrella know?
Plot hole: When the umbrella ops first get onto the train, rain has to power it up. There were plugs disconnected, and you see a hole in the fence as she shines a flashlight on it. It can't be anything infected because they didn't power down the red queen yet, and release the bioweapons. The red queen isn't physical, just controls systems. And with none of the zombies, or other infected loose yet, what else could have unplugged it? Spence was knocked out on the train, this seems to be a plot hole. (00:02:00 - 00:20:10)