Flora 'knew' Miles was coming home?
Many of the posts that support there being actual ghosts use the fact that Flora "knew" Miles was coming home as support for their theory, because all other events were ONLY from Miss Giddens point of view.
However this can be easily explained by the fact that Flora must have been saying "Miles is coming home" from the moment he left, as she would desperately want him home, being an orphaned little girl alone in the world. She must have been distraught that he was being sent away and that they were being separated as they only had each other. And he must have promised her that he would get himself thrown out of that boarding school full of rules and regulations (if he was anything like his uncle) and back home. Because he was so precocious and sexualized at a young age it would be easy for him to break all rules and return home to his sister. He might even have sent letters to this effect to Flora. AND ALSO Flora must have known that when the new governess was HIRED that her brother would be returning soon.
It is very clear on a second viewing of this movie especially from the very first scene of miss Giddens crying and praying, that this is a psychological thriller, rather than a ghost story. It is all from Miss Giddens point of view, this repressed psychologically fragile unstable woman being exposed to unfamiliar surroundings, and children who were far from innocent, who were damaged and sexualized in a way that Miss Giddens could not comprehend or deal with.