Theory

Sorry if this has been stated already, I tried to skim through and didn't see it yet.

Xavier’s wife was purposely left off that plane to die.

Xavier mentions in episode 1, that his wife is a scientist working on a new project down in Atlanta.

The show leads us to believe she wasn't able to board the plane on time. Now she might be still alive, but that would take the show in a different direction, something similar to the village.

I think Sinatra wanted as little scientists as possible. Because eventually they would start theorizing how to move back out into the open world. Which is why she killed off the 4 that were sent outside.