Contradiction with Numbers 26:54
Joshua 17:1 states that a lot fell to the tribe of Manasseh, whereas Numbers 26:54 deals with the land distribution determined by the size of the tribe.
Numbers 26:54: To many thou shalt give the more inheritance, and to few thou shalt give the less inheritance: to every one shall his inheritance be given according to those that were numbered of him. [give the more...: Heb. multiply his inheritance] [give the less...: Heb. diminish his inheritance]
Contradiction with Joshua 14:4
Joshua 17:1 discusses the inheritance of Manasseh including Gilead, but Joshua 14:4 states that the Levites received no land inheritance beyond cities.
Joshua 14:4: For the children of Joseph were two tribes, Manasseh and Ephraim: therefore they gave no part unto the Levites in the land, save cities to dwell [in], with their suburbs for their cattle and for their substance.
Contradiction with Deuteronomy 3:13
Joshua 17:1 emphasizes inheritance for Machir, son of Manasseh, yet Deuteronomy 3:13 suggests this was already allotted by Moses to the half-tribe of Manasseh.
Deuteronomy 3:13: And the rest of Gilead, and all Bashan, [being] the kingdom of Og, gave I unto the half tribe of Manasseh; all the region of Argob, with all Bashan, which was called the land of giants.