That really annoyed me too. Fran was the one who actually got injured and they don't even ask about her! To be fair though they might not have known she was there, because Balthier and Fran say they are going to the engine room. But they should have made an educated guess that where Balthier is Fran is.

In regards to Revenant Wings, Balthier does seem to be a little more protective of Fran than he used to be. He makes her wait at the Strahl so as not to get afflicted by the mist. Maybe seeing her get squished made him worry