​Please tap on this building, choose "owner" and see if you can choose one of your cities as its owner. 

Buildings like harbor, village, resource zone, all need a nearby city as owner. If it has no owner city, that means you need to capture a nearer city to own it.  If captured buildings have no city as owner city, they actually are dead. Village can't generate fortune, resources zone won't provide resources, and no building can be built on them cause no population and steel can be taken from any of your cities.