John Gill 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)

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 17:8Joshua 17:9) ;

all the cities with their villages ;
not the separate cities only, but the little towns adjacent to them.