Something like that. There's nothing special about ferries that would make them magically immune to being captured.
I would have thought that boarding a ferry would make someone more difficult to capture. Yet I know that the game does not work that way.
I am just trying to imagine what actually happened to my character. So she boarded, got a good captain to go fast, and then got captured anyway, but her unit is still on board... or something. Puzzling, huh?