This isn't a bug, it's just the result of some rule changes and the Civilization tech tree being disabled. If you want your cities to grow, you'll need to find food resources that can be harvested without research, such as oases. You can create them with the Restore Garden spell, if you like. In addition, your gardens produce 3 food while a hut only consumes 2, so if you build a second garden in a second city, you'll be able to afford an extra hut.
