I'm not exactly sure that only these create such things in-game but they're probably involved.

This is what's happening:

Here's the list of mods I have installed and their load order. Perhaps the load order is wrong or something else is but I'm really not sure. Anyone else encountered similar things in the past? How did you fix it?

Simply, you can't use them both! You need to use better cities "open" version (included in the better cities package)