Contradiction with Exodus 33:20
Nehemiah 9:13 states that God spoke openly and directly with the Israelites at Mount Sinai, whereas Exodus 33:20 suggests that no one can see God's face and live, implying a less direct form of communication.
Exodus 33:20: And he said, Thou canst not see my face: for there shall no man see me, and live.
Contradiction with Deuteronomy 4:12
Nehemiah 9:13 implies direct communication from God to the people, while Deuteronomy 4:12 mentions that they heard a voice but saw no form, which may imply an indirect interaction.
Deuteronomy 4:12: And the LORD spake unto you out of the midst of the fire: ye heard the voice of the words, but saw no similitude; only [ye heard] a voice. [only...: Heb. save a voice]
Contradiction with 1 Kings 19:11-12
Nehemiah 9:13 depicts God as giving laws openly to the Israelites, while in 1 Kings 19:11-12, God's presence is portrayed as subtle, through a gentle whisper, rather than direct proclamation.
1 Kings 19:11-12: And he said, Go forth, and stand upon the mount before the LORD. And, behold, the LORD passed by, and a great and strong wind rent the mountains, and brake in pieces the rocks before the LORD; [but] the LORD [was] not in the wind: and after the wind an earthquake; [but] the LORD [was] not in the earthquake: