Albert Barnes Commentary Joshua 16:9

"together with the cities which were set apart for the children of Ephraim in the midst of the inheritance of the children of Manasseh, all the cities with their villages." — Joshua 16:9 (ASV)

The verb "were," introduced by the King James Version in this verse, should be omitted, and the period after Joshua 16:8 replaced by a colon. The meaning 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 was found to be too small. Therefore, some towns, which are named in 1 Chronicles 7:29, were given to them from the kindred Manassites, with the latter being compensated (see the note on Joshua 17:11) at the expense of Issachar and Asher.