The tribe of Manasseh faced significant military and territorial hurdles when attempting to take full control of their designated land. Even though they were granted additional territories within the borders of the tribes of Issachar and Asher—allocations that Joshua would formalize later—they were ultimately unable to conquer these regions [מלבי״ם].
Their efforts to take possession of the land involved attempts to capture fortified cities and either expel or destroy the local inhabitants [ביאור שטיינזלץ]. However, because the tribe of Manasseh failed to complete this mission, the local Canaanite population remained. The primary approach among commentators is that the Canaanites actively willed and agreed to stay. Rather than being driven away, they made a deliberate choice, and simply persisted in living and settling freely within the territory [ביאור שטיינזלץ].