FP2 ending was.. really weird.

So I started the game trying to appease everyone but supported Faithkeepers on every turn and kept Evolvers down. They never got above 4% but in the end were only like 170 out of 50k total while Faithkeepers were 91% and absolutely loved me since I kept passing everything they wanted and had baptisms and other positive things on cooldown.

I was generally as nice as possible and didn't do anything too drastic. Live and let live. Gave the woman her book back and let it slide when she made it sarcastic and about me. Gave all the factions (except for Evolvers) agendas and listened to them etc.

After Winterhome was salvaged though, all hell broke loose. I saw it coming and though that how much cause those 100ish thugs really do? Well it turned out quite a lot actually. In the end I had 25% put into prison district but I tried to make it comfortable and Lily May ended smuggling food and living there with her mom somehow.

So who the hell are those 25%, or over 10k people there anyway? There weren't that many non Faithkeepers in the city to begin with and I never really give them any reason to dislike me, supporting them on almost every single turn. Even before becoming captain trust was maxed out and discontent was zero.

So what exactly happened there?