Turrets are supposed to stop firing when a non-hostile crosses it, they added this long time ago. What OP describes sounds like a bug, he should ticket it and ask for his credits back.
Or... do political assassinations and have a radar full of flashing red dots become normal.
So if you do use turrets excessively, don't care about who you hit- they're only system security after all. Learning how to take a couple down for giggles before you wake out might improve combat skills.