Be them transsexual, bigender, neutrois, or whatever sort of transgendered. Do you refer to them by their correct pronouns, or by their sex?
There seems to be some sort of drift among fans of series when it comes to transpeople, usually depending on how direct it is. If its a prominent feature and they've transitioned, then it's likely that they'll be called the proper pronouns. If not.. Then its in the air basically.
For example.. Say, Wandering Son vs Parrotfish. They both center around transsexual children, but with the former its more likely for people to call them crossdressers.
I've recently been reading about a manga named Black Butler. I haven't begun reading or watching it yet, since I'd prefer to buy the volumes.
For months I thought Grell was a flamboyant gay crossdresser, because that's how people made them sound. Turns out Grell is a very explicitly out transwoman, albeit pre-op.
I've heard a lot of people say it doesn't matter if you refer to them by the correct pronouns, especially if in-series people refer to them by the opposite. It'll "confuse new fans" or whatnot. I always make it a point to refer to a character by what seems to be their gender. You don't see that many transgendered characters that aren't cross-dressers or transsexual, so I've never really had to use any other pronouns though.