Contradiction with 2 Peter 3:9
John 12:39 suggests people could not believe because God blinded their eyes, while 2 Peter 3:9 emphasizes God's patience and desire for everyone to come to repentance.
2 Peter 3:9: The Lord is not slack concerning his promise, as some men count slackness; but is longsuffering to us-ward, not willing that any should perish, but that all should come to repentance.
Contradiction with Ezekiel 18:32
John 12:39 indicates a divine hardening preventing belief, whereas Ezekiel 18:32 shows God's preference for the wicked to turn and live.
Ezekiel 18:32: For I have no pleasure in the death of him that dieth, saith the Lord GOD: wherefore turn [yourselves], and live ye. [yourselves: or, others]
Contradiction with 1 Timothy 2:4
John 12:39 implies God's role in disbelief, yet 1 Timothy 2:4 states that God wants all men to be saved and to come to knowledge of the truth.
1 Timothy 2:4: Who will have all men to be saved, and to come unto the knowledge of the truth.
Contradiction with Romans 10:13
John 12:39 implies inability to believe, but Romans 10:13 assures that everyone who calls on the name of the Lord shall be saved.
Romans 10:13: For whosoever shall call upon the name of the Lord shall be saved.
Contradiction with James 1:13
John 12:39 suggests God's involvement in disbelief, while James 1:13 asserts that God does not tempt anyone to sin.
James 1:13: Let no man say when he is tempted, I am tempted of God: for God cannot be tempted with evil, neither tempteth he any man: [evil: or, evils]
Contradiction with Matthew 11:28
John 12:39 indicates inability to come, while Matthew 11:28 invites all who are weary to come to Jesus and find rest.
Matthew 11:28: Come unto me, all [ye] that labour and are heavy laden, and I will give you rest.