My Assault Crusader "Noshijobu" is stuck on the quest Saving Caius Thorn. I have to search 3 locations for Magos Biologis but I can't find her/continue the quests. It's weird though because even though she is not on my command deck, she speaks to me during these Aethon missions (even though I am still "searching for her"). 

I was in a co-op story mission with a sister of battle searching for the Magos Biologis before this, which I believe is the cause of the bug.