The separate cities — That is, besides those cities which were within Ephraim's bounds, he had some other cities, to which all of all their territories were annexed out Manasseh's portion, because his tribe was all here, and was larger than Manasseh's.
Related Commentaries of Joshua 16:9
Joshua 16:9
9 And the separate cities for the children of Ephraim were among the inheritance of the children of Manasseh, all the cities with their villages.