And there were cities with their villages separated for the children of Ephraim in the midst of the possession of the children of Manasses.

with the cities that were set apart for the children of Ephraim in the midst of the inheritance of the children of Manasseh, all the cities and their hamlets.

together with the cities which were separated for the children of Ephraim in the midst of the inheritance of the children of Manasseh, all the cities with their villages.

Together with the towns marked out for the children of Ephraim in the heritage of Manasseh, all the towns with their unwalled places.

And there were cities, with their villages, which were set aside for the sons of Ephraim, in the midst of the possession of the sons of Manasseh.

Et urbes separatae filiis Ephraim in medio haereditatis filiorum Manasse, omnes urbes, et villae earum.

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.

And the separate cities - That is, the cities that were separated from the tribe of Manasseh to be given to Ephraim; see Joshua 17:9.

And the (e) separate cities for the children of Ephraim [were] among the inheritance of the children of Manasseh, all the cities with their villages.
(e) Because Ephraim's tribe was far greater than Manasseh, therefore he had more cities.

And the separate cities for the children of Ephraim,.... The tribe of Ephraim, being much larger than the half tribe of Manasseh, besides the lot that fell to it, described before by its boundaries, had several particular and distinct cities given to it: which
were among the inheritance of the children of Manasseh; some that were upon the borders of Ephraim, and within the territory of Manasseh, and it may be where it jetted out in a nook or corner, see Joshua 17:8,
all the cities with their villages; not the separate cities only, but the little towns adjacent to them.

separate cities for the children of Ephraim were among the inheritance of Manasseh-- (Joshua 17:9), because it was found that the tract allotted to Ephraim was too small in proportion to its population and power.

The tribe of Ephraim also received some scattered towns in the territory of the tribe of Manasseh, in fact all those towns to which Tappuah belonged, according to Joshua 17:8, with the dependent villaGes.
(Note: The reason why the Ephraimites received scattered towns and villages in the tribe-territory of Manasseh, is supposed by Calvin, Masius, and others, to have been, that after the boundaries had been arranged, on comparing the territory allotted to each with the relative numbers of the two tribes, it was found that Ephraim had received too small a possession. This is quite possible; at the same time there may have been other reasons which we cannot discover now, as precisely the same thing occurs in the case of Manasseh (Joshua 17:11).)

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.