Contradiction with Numbers 1:3
Contradicts the order in Mark 6:40 by emphasizing the organization of people based on military service from ages twenty and upward.
Numbers 1:3: From twenty years old and upward, all that are able to go forth to war in Israel: thou and Aaron shall number them by their armies.
Contradiction with 1 Corinthians 14:33
Contradicts by stating that God is not the author of confusion, whereas Mark 6:40 describes a scenario that might seem chaotic due to the sheer number of people needing organization.
1 Corinthians 14:33: For God is not [the author] of confusion, but of peace, as in all churches of the saints. [confusion: Gr. tumult, or, unquietness]
Contradiction with Matthew 14:21
While describing a similar event, does not emphasize the detailed organization by ranks of hundreds and fifties, thus contradicting the specificity in Mark 6:40.
Matthew 14:21: And they that had eaten were about five thousand men, beside women and children.
Contradiction with 1 Peter 5:3
Contradicts by highlighting leadership by example, not by compulsion, contrasting with the structured seating arrangement in Mark 6:40.
1 Peter 5:3: Neither as being lords over [God's] heritage, but being ensamples to the flock. [being lords over: or, overruling]