Yes, the town I planted was quite new and 100% sure it's during monarchy! Therefore I never whiped there anything, I couldn't even do it. I even double checked the saves, and it's true... yes, I rushed the temple but paid in hard cash like every enlightened monarch does...

So, what happened?
1. it's a bug
2. whipped settlers could transfer the discontent (I'm not sure if the particular settler was whipped but it was very possible)
3. there was a city one hex down I razed one day, could it be they somehow "remember" it?