I was let on the wrong United flight at London Heathrow a few years ago. There were two flights to the US leaving about the same time. It was only discovered when the correct passenger boarded, found his seat and I was sitting in it!
That is what Japanese news is saying happened here as well. This passenger ended up on the wrong flight and was only discovered three hours later because he was seated in the chair reserved for flight attendants. Which is plausible I suppose if he hadn’t paid for a ticket to Japan even on another airline.