Contradiction with Matthew 6:5
This verse advises against public displays of prayer for the sake of being seen by others, contradicting the public nature of the prayer gathering in Nehemiah 9:4.
Matthew 6:5: And when thou prayest, thou shalt not be as the hypocrites [are]: for they love to pray standing in the synagogues and in the corners of the streets, that they may be seen of men. Verily I say unto you, They have their reward.
Contradiction with 1 Timothy 2:8
This verse encourages prayer without wrath and doubting, which might conflict with the mood of confession and penitence suggested in Nehemiah 9:4.
1 Timothy 2:8: I will therefore that men pray every where, lifting up holy hands, without wrath and doubting.
Contradiction with Matthew 6:6
Advocates for private prayer, in contrast to the public calling upon the assembly seen in Nehemiah 9:4.
Matthew 6:6: But thou, when thou prayest, enter into thy closet, and when thou hast shut thy door, pray to thy Father which is in secret; and thy Father which seeth in secret shall reward thee openly.