Elite: Dangerous PvE - Mobius

I have been doing missions for the federation faction in Abrocmii (Social Abrocmii Future) and in Witchaul (Witchaul Corporation). When I do missions for the federation faction in Abrocmii, my federation faction goes down as does my reputation for the local federation faction in Witchhaul.

Why does doing missions for a federation aligned faction give me negative reputation for the federation globally and locally?

I think there is a civil war going on at the moment with Witchaul, that may have some bearing on it, but until FD open "The Black Box" and tell us what the actual dynamics are, we can only guess