I was playing as the Romans (current year 213 BC), and I've noticed once after loading a save and playing a few turns that all of my government buildings (i.e. Regional Pacification & Romanized Province and such) were destroyed. I repaired all of them, saved, and called it a night. The next day when I loaded it up again I played a couple turns and all those buildings were destroyed again.

Also, while playing as the Casse last night, I noticed the same thing. I clicked on the city and everything was undamaged in the city, as soon as I activated the script, the government building (Casse version of Regional Pacification) was destroyed in this city and all my other cities.