Missed edit window:
Alternatively, you may have had brush with SCP-342.
Well, I once had somebody ask me, on a fairly empty bus, if the seat next to me was occupied (it obviously wasn’t) and, feeling kind of frisky that day I replied, “Oh my god, you mean you can’t SEE him?”
The guy moved on and sat somewhere else.
I really hope Shagnasty’s story spreads like wildfire, eventually showing up at the snopes website. It positively screams urban legend.
Go on – Google “James O’Mallie Chicago ghost”, and see what you find. 
Geez, I would have been all over that. I love meeting fun people on the train.
Of course, around here, nobody asks permission. If there’s an empty seat, you take it.