Ok, I checked the save, and it's exactly the problem I was talking about.
City at north, due to resources linking to city walls expanded so much southwards that all buildable tiles for city at south now fall into less then 5 tiles into distance from the northern city. And, as game rule, you can't build buildings on tiles that are less then 5 tiles away from other city (counting from closest city wall). That's also why even destroying buildings in southern city won't free place for new buildings.
To demonstrate the issue, destroy south lost library, and you will be able to build things in other city, but only in locations at south. Destroy gold mine too, and you'll get more tiles free.
P.S.
And yes, whole system sucks.