I created a custom faction with Allayi affinity. I gave them Weapons of the Enemy trait (immediately destroy captured cities).

When I reach chapter 8 of the Faction Quest ("Fate of Auriga"), it says that I must capture 3 cities.

I declare war and capture 3 cities, but the captured cities did not count. Of course each city was immediately destroyed because of Weapons of the Enemy.

The quest said "capture 3 cities". It did not say "capture and HOLD 3 cities".
So basically if I take Weapons of the Enemy, the Allayi faction quest is impossible to complete, unless capturing and destroying is also counted.
It was very frustrating because I worked hard to complete the faction quest only for this problem to appear and make it impossible to complete. It was totally beyond my control and impossible to predict. Can this be fixed?