Manasseh was not able to defeat those cities, so the Canaanites continued to live there.
They were descendants of people that the Israelites had not destroyed. Solomon forced them to work for him as slaves, as is still true today.
The army of Judah was not able to force out the Jebusites living in Jerusalem, so the Jebusites still live among the people of Judah to this day.
The Ephraimites could not force the Canaanites to leave Gezer, so the Canaanites still live among the Ephraimites today, but they became slaves of the Ephraimites.