Sometimes a resource (Clay Pit/Iron Mine/Earth Shard/whatever) or Outpost will bind to the wrong city.  It's obviously closer to another city than the one it bound to.  Also, it might be inside the ZoC of the nearest city, and outside of the ZoC of the city it binds to instead.   I have a screenshot here that illustrates both of those (I touched it up a bit to highlight it).

I also have a savegame I made right at this time.  The Clay Quarry wasn't done being built yet, so you can cancel it and restart it if that helps somehow.  http://darkseam.com/fe/Resource_Wrong_City.EleSav

I've had this experience several times in FE as well, but I'd never gotten such a perfect example before.