I can't add a note yet to the other poster.
The WAU actually kills people. That's what doesn't make sense.
It brings back Simon when it could have easily brought back others--even multiple times of the same copy.
It kills everyone at Omicron by bursting their blackboxes (why they have no heads) because Dr Ross had telepathically instructed Herber to create the virus-structure gel and attempt to bring it to Alpha and kill the WAU.
Perhaps the WAU only kills people "in their best interest" because it the WAU's mind, if it dies, humanity dies, so it's okay to kill some humans.
There is one line I think that's important to understanding this (though I'm still missing a couple more clues): Dr Ross said the WAU doesn't understand the difference between humans and robot-humans--which is why he wants to kill it. That seems like an important clue to why the WAU is acting the way it is. Another clue they give us is that the WAU changed to a "simpler protocol" version of protect humanity once humanity on the surface died.
It also doesn't make sense why it corrupts the station, corrupts itself, or creates robot versions of people that then go insane and murder each other. If the WAU can detect the dead, and try to prevent it, surely it can detect when it's creations either go insane, or start murdering normal humans.
It's also not clear why Ross was the only one "brought back" (other than Simon) that didn't go insane. And how the WAU placed a cortex chip in the body of a diving suit--as opposed to simply scanning Simon's brain into the machines like it did the rest of the brains.