We can't destroy buildings ever ever ever ever. So the script has to put one in for the AI factions each time a new one conquers a province (as their bonuses are restricted to only that one faction). Don't worry about the remains of previous governments - just destroy them all when you finally take it over.
Jebus - the problem has now been noted. I don't think I can get a new change in for the next patch, but we will just remove it for the time being. It's supposed to be another unique building, but we switched the culture for the province and it flipped it into Dodone (it's the same building actually). Thanks for noting it.
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