Contradiction with Joshua 13:1
Joshua 13:1 states that land remains to be conquered, which contradicts Joshua 12:7 that lists the kings defeated by Joshua, suggesting a completed conquest.
Joshua 13:1: Now Joshua was old [and] stricken in years; and the LORD said unto him, Thou art old [and] stricken in years, and there remaineth yet very much land to be possessed. [to...: Heb. to possess it]
Contradiction with Judges 1:21
Judges 1:21 mentions the Jebusites dwelling with the children of Benjamin in Jerusalem, conflicting with the complete conquest implied in Joshua 12:7.
Judges 1:21: And the children of Benjamin did not drive out the Jebusites that inhabited Jerusalem; but the Jebusites dwell with the children of Benjamin in Jerusalem unto this day.
Contradiction with Judges 1:27
Judges 1:27 states that Manasseh did not drive out the inhabitants of certain cities, opposing the narrative of a comprehensive victory in Joshua 12:7.
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 Numbers 33:55
Numbers 33:55 warns Israel that if they do not drive out the inhabitants, they will be a problem, implying incomplete conquest, contrasted with the list of victories in Joshua 12:7.
Numbers 33:55: But if ye will not drive out the inhabitants of the land from before you; then it shall come to pass, that those which ye let remain of them [shall be] pricks in your eyes, and thorns in your sides, and shall vex you in the land wherein ye dwell.
Contradiction with Joshua 23:13
Joshua 23:13 predicts that nations will remain as a snare, contradicting the idea of total victory as suggested in Joshua 12:7.
Joshua 23:13: Know for a certainty that the LORD your God will no more drive out [any of] these nations from before you; but they shall be snares and traps unto you, and scourges in your sides, and thorns in your eyes, until ye perish from off this good land which the LORD your God hath given you.