I completely forgot about this until I saw an off-hand mention of prison space on another thread, but... is it intentional that your prisons never get filled? I captured a whole bunch of enemies on my previous playthrough, dozens and dozens, and never got any prisoner management screen or anything like that. When I checked the prison it showed I had negative space, but I never had to do anything about it.
I think at the time I assumed it must be intentional because of how the interrogating live prisoners thing is bloated by all the dossiers, but I figured it was worth checking.