Contradiction with Joshua 11:15
This verse states that Joshua left nothing undone that the Lord commanded Moses, while Joshua 11:3 speaks of various inhabitants being targeted for destruction, suggesting completeness without contradiction.
Joshua 11:15: As the LORD commanded Moses his servant, so did Moses command Joshua, and so did Joshua; he left nothing undone of all that the LORD commanded Moses. [left...: Heb. removed nothing]
Contradiction with Joshua 13:13
This verse states that the children of Israel did not drive out the Geshurites and Maachathites, which seems to contradict the implication of comprehensive conquest in Joshua 11:3.
Joshua 13:13: Nevertheless the children of Israel expelled not the Geshurites, nor the Maachathites: but the Geshurites and the Maachathites dwell among the Israelites until this day.
Contradiction with Judges 1:27
It explains that Manasseh did not drive out the inhabitants of certain regions, opposing the idea in Joshua 11:3 that all inhabitants were conquered.
Judges 1:27: Neither did Manasseh drive out [the inhabitants of] Bethshean and her towns, nor Taanach and her towns, nor the inhabitants of Dor and her towns, nor the inhabitants of Ibleam and her towns, nor the inhabitants of Megiddo and her towns: but the Canaanites would dwell in that land.
Contradiction with Judges 1:29
States that Ephraim did not drive out the Canaanites, contradicting Joshua 11:3 where there's an impression of widespread conquest.
Judges 1:29: Neither did Ephraim drive out the Canaanites that dwelt in Gezer; but the Canaanites dwelt in Gezer among them.