The Jebusites lived in Jerusalem, and the people of the Judah tribe could not capture the city and get rid of them. That's why Jebusites still live in Jerusalem along with the people of Judah.
Ephraim could not force the Canaanites out of Gezer, so there are still some Canaanites who live there among the Israelites. But now these Canaanites have to work as slaves for the Israelites.