So on my main save, I went into origin mode and noticed how it had a really weird pattern and saw how one nation that shouldn't have existed still had an origin. I united two countries so one should have disappeared but it didn't. Similarly, another nation also had an incorrect origin that had no connection to it, like it was never part of the one country that it had the origin of. I then noticed that the problem was that there were 2 leaders for the same country for whatever reason and the different leaders overlapped with the changed origins. They were still the same country and the leaders had the same trait it's just that they were different names and different cultures.