the FA's dont pay much attention to who is sitting where, i doubt that they even realized the seat went from open to occupied.
this is a tough one, for me i'd probably make discreet mention of it to the FA by making a trip to the galley. if they chose not to do anything about it, i'd let it go and report it later via email. part of my benefits that i pay a lot of money for is comp E+, and a fringe benefit of that is often having an open middle seat next to me. my inclination is that i would defend that benefit, particularly on a flight this long if i found myself in coach.