I've got a captured city that is permanently stuck at level 1, and the AI built a bunch of cities nearly on top of one another. One set is literally within 5 squares of the next.
I've also got cities that can build a Construction Yard, and some that can't without any indication why. None of my cities can build the Tower of Iziz(I think that's it's name), and my construction techs seem to do absolutely nothing. A Hedge Wall takes me 20 turns to build before and after a construction yard.
I'm also seeing no effect from pubs or town halls, no expansion of influence.
In short, I'm noticing a few bugs here with cities.