The verb “were,” introduced by the King James Version in this verse should be omitted; and the full stop after Joshua 16:8 replaced by a colon. The purport of Joshua 16:9 is simply to add to the inheritance of Ephraim, defined by the preceding context, “the separate cities” or more properly “single cities” which were allotted to them in addition within the borders of Manasseh. The reasons for granting these additional cities to the Ephraimites can only be conjectured. Perhaps the territory assigned to this numerous tribe proved on experiment to be too small; and therefore some towns, which are named in 1 Chronicles 7:29, were given to them from the kindred Manassites, the latter being recompensed (Joshua 17:11 note) at the expense of Issachar and Asher.
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.