Rage time.
(Don't take this personally.)
A lot of the things you listed as poltholes were explained in the game, they just didn't make a gigantic deal out of it. If there was something that wasn't really there it was kind of nice because you could either figure it out yourself our add your own little part to the story. I'm glad that they didn't tell you everything you can do in the game, because that would make experimenting impossible. That cutscene you were talking about isn't really supposed to be taken literally. It's more just to show the horror they lived through. I think you might be skipping parts of the story by accident. All the things you didn't understand I knew them perfectly.