So I took a look at this, besides the Unrest, some settlements just have a high base farming level meaning more population which means more Squalor, and harder to get garrison effect.
Interestingly, happiness and especially health increase population growth rate, which also causes problems with Squalor and garrisons. Specifically, while:
- 10% law (in building description) -> +5% Public order
- 10% Happiness -> +1.75% PO (after squalor effect)
- 10% Health -> +1.4% PO (after squalor effect)
- 1% growth -> -0.45% PO (after squalor)
One useful trick is to get someone with plague and then carefully** plague your cities, reducing their population without the need to reconquer etc. Also, going for max Law and minimum population (so as little Happiness, Health, growth as possible) and just putting tons of peasants in to keep it at Very High taxes may also work...
My campaign amusingly turned into this population control simulator where I starve Italy (destroying farms....) but tax it at Very High forever.
** If you can sacrifice some small town or castle, keep some... Diplomats? And just keep on reinfecting it/them with plague then use them to control populations.