I had assumed that Harley had been free and snuck into Arkham to take over the security systems. She was wearing the weird nurse-thing outfit as part of the theme.
Bane being in costume is sort of justified. I haven't gotten to Ivy yet, but I remember seeing a trailer and she was wearing a bright orange prison-issue top (and foliage for a bottom).
Tangently, every time I hear Oracle in the game, I wonder "Has Bluefall played this yet? 'Cause Babs is pretty good here."