Contradiction with John 3:16
John 11:49 has a high priest speaking of death as a necessity, seemingly contradicting the message of love and salvation in John 3:16.
John 3:16: For God so loved the world, that he gave his only begotten Son, that whosoever believeth in him should not perish, but have everlasting life.
Contradiction with Matthew 9:13
John 11:49 suggests a death for the greater good, while Matthew 9:13 emphasizes God's desire for mercy over sacrifice.
Matthew 9:13: But go ye and learn what [that] meaneth, I will have mercy, and not sacrifice: for I am not come to call the righteous, but sinners to repentance.
Contradiction with Hebrews 10:10
John 11:49 implies a human reasoning for sacrifice, in contrast to the divinely perfect will described in Hebrews 10:10.
Hebrews 10:10: By the which will we are sanctified through the offering of the body of Jesus Christ once [for all].
Contradiction with Acts 5:29
John 11:49 reflects human counsel for an action, opposing Acts 5:29 which asserts the need to obey God rather than human plans.
Acts 5:29: Then Peter and the [other] apostles answered and said, We ought to obey God rather than men.
Contradiction with James 3:17
John 11:49 discusses a seemingly pragmatic decision, whereas James 3:17 emphasizes wisdom from above as pure, peaceable, and gentle.
James 3:17: But the wisdom that is from above is first pure, then peaceable, gentle, [and] easy to be intreated, full of mercy and good fruits, without partiality, and without hypocrisy. [partiality: or, wrangling]
Contradiction with 1 John 4:8
John 11:49 involves a death for a perceived greater good, contrasting with the overarching theme of God's love central in 1 John 4:8.
1 John 4:8: He that loveth not knoweth not God; for God is love.
Contradiction with Romans 12:19
John 11:49 has a high priest taking matters into human hands, contrary to Romans 12:19 which advises leaving vengeance to God.
Romans 12:19: Dearly beloved, avenge not yourselves, but [rather] give place unto wrath: for it is written, Vengeance [is] mine; I will repay, saith the Lord.