I've reported this issue earlier and got no response.
How to reproduce: Eliminate all empire factions before Istiana's conspiracy reaches 2000. Leading clans will join other factions and when conspiracy reaches 2000, one of them will declare war on you, even tho they don't exist anymore.
In my case, I was playing with Vlandia and Southern Empire declared war on us, even tho they were destroyed earlier and Rhagea already joined Vlandia as a vassal.
Main quest is just too buggy at the moment. Better steer clear of it for the time being.