Contradiction with Joshua 11:3
Joshua 11:3 lists the Hivites as among those who did fight against Israel, unlike Joshua 9:1, where they are implied to be preparing to fight but later make peace deceitfully with Israel.
Joshua 11:3: [And to] the Canaanite on the east and on the west, and [to] the Amorite, and the Hittite, and the Perizzite, and the Jebusite in the mountains, and [to] the Hivite under Hermon in the land of Mizpeh.
Contradiction with Joshua 11:19
This verse indicates that all other cities besides Gibeon (home of the Hivites) did fight against Israel, suggesting that others were not preparing to fight as implied in Joshua 9:1.
Joshua 11:19: There was not a city that made peace with the children of Israel, save the Hivites the inhabitants of Gibeon: all [other] they took in battle.
Contradiction with Exodus 23:31-32
This passage suggests that God commanded the Israelites to drive out the inhabitants of the land and not make any covenants with them, contradicting the implication of an impending battle with those enemies in Joshua 9:1.
Exodus 23:31-32: And I will set thy bounds from the Red sea even unto the sea of the Philistines, and from the desert unto the river: for I will deliver the inhabitants of the land into your hand; and thou shalt drive them out before thee.
Contradiction with Deuteronomy 20:16-18
The instruction to completely destroy the inhabitants as a form of conquest is contrasted by the preparation for an alliance or deceit indicated in Joshua 9:1.
Deuteronomy 20:16-18: But of the cities of these people, which the LORD thy God doth give thee [for] an inheritance, thou shalt save alive nothing that breatheth:
Contradiction with Judges 1:21
This verse states that the Jebusites were not driven out by the Israelites, which contradicts the notion in Joshua 9:1 that they were actively in conflict with Israel.
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 Numbers 33:52-53
Command to dispossess the inhabitants of the land conflicts with the preparation for combat by multiple groups detailed in Joshua 9:1.
Numbers 33:52-53: Then ye shall drive out all the inhabitants of the land from before you, and destroy all their pictures, and destroy all their molten images, and quite pluck down all their high places: