The Anakites were known for their size and fortified cities (see Numbers 13:33; Deuteronomy 9:2; Joshua 14:12).1 According to Joshua 11:21–22, the Anakites have already been destroyed by the armies of Israel and driven from Hebron (see Joshua 10:3, Joshua 10:36–37; Joshua 12:10). It may be that some of them went to hide in Gaza, Gath, and Ashdod before moving back into the area.2
We should also consider that with forty-five years having elapsed since the forty-year judgment of wilderness wandering (Numbers 14:33–34), the various campaign battles recounted in Joshua 1:1 – 12:24 took place over five or seven years (seven years if you include the two years before the spies' report from Numbers 10:11). There would thus have been time for some of the Anakite survivors to regroup and occupy their city when the Israelites moved on to fight elsewhere.
12 So now give me this hill country of which the LORD spoke on that day, for you heard on that day how the Anakim were there, with great fortified cities. It may be that the LORD will be with me, and I shall drive them out just as the LORD said.”