What does it mean when an otherwise empty city has sections of it shaded red, accompanied by text saying that you can't build in that area? Is it an area where a facility is currently being built? If so, where are the builders?
Ongoing construction shows up as yellow and black stripes. Is the city in question in a cave? I recall reading on the Rules pages that caves have unbuildable areas due to stalactites/stalagmites, etc. Since I haven't seen the phenomenon, I suspect this is what you're encountering, but can't be sure.
"May the Grace of Ara go with you, and His Vengeance be wrought upon your enemies."