Well shit.
I don't know why but in mind I was thinking it was fighting at night would cause your ships to sink. She had taken critical damage in a previous battle so that explains it.
I thought that at first until I read otherwise. I think you lose morale through night battles and you can take much more damage, so if you ever want to get to a boss node it's probably best to ignore them. You can get drops from rank b and above so it's fine to just leave a battle.