Contradiction with Deuteronomy 19:2
Contradicts Joshua 20:7 by specifying a different set of cities intended for refuge, suggesting a reallocation or reassignment may have occurred.
Deuteronomy 19:2: Thou shalt separate three cities for thee in the midst of thy land, which the LORD thy God giveth thee to possess it.
Contradiction with Exodus 21:14
Contradicts the idea of cities of refuge by stating that anyone who kills their neighbor with intent should be taken from an altar and put to death, implying no refuge should be given for certain acts of violence.
Exodus 21:14: But if a man come presumptuously upon his neighbour, to slay him with guile; thou shalt take him from mine altar, that he may die.
Contradiction with Numbers 35:31
Contradicts the establishment of cities of refuge for fleeing murderers by stating that no satisfaction shall be taken for the life of a murderer, indicating an absolute punishment instead of asylum.
Numbers 35:31: Moreover ye shall take no satisfaction for the life of a murderer, which [is] guilty of death: but he shall be surely put to death. [guilty...: Heb. faulty to die]
Contradiction with Deuteronomy 4:41-42
Lists different locations for cities of refuge east of the Jordan, creating a contradiction with Joshua 20:7 which details cities west of the Jordan.
Deuteronomy 4:41-42: Then Moses severed three cities on this side Jordan toward the sunrising;
Contradiction with 2 Samuel 3:27
Describes Joab killing Abner in the city of refuge of Hebron, contradicting the safety supposedly ensured by cities like the ones listed in Joshua 20:7.
2 Samuel 3:27: And when Abner was returned to Hebron, Joab took him aside in the gate to speak with him quietly, and smote him there under the fifth [rib], that he died, for the blood of Asahel his brother. [quietly: or, peaceably]