Contradiction with Exodus 32:1
Exodus 40:16 states that Moses did everything as commanded by the Lord, but Exodus 32:1 shows the Israelites asking Aaron to make gods when Moses delayed coming down from the mountain, implying disobedience.
Exodus 32:1: And when the people saw that Moses delayed to come down out of the mount, the people gathered themselves together unto Aaron, and said unto him, Up, make us gods, which shall go before us; for [as for] this Moses, the man that brought us up out of the land of Egypt, we wot not what is become of him.
Contradiction with Numbers 20:11-12
In Exodus 40:16, Moses obeys as commanded, but in Numbers 20:11-12, he strikes the rock twice instead of speaking to it, which leads to God's reprimand.
Numbers 20:11-12: And Moses lifted up his hand, and with his rod he smote the rock twice: and the water came out abundantly, and the congregation drank, and their beasts [also].
Contradiction with Exodus 16:20
Exodus 40:16 highlights Moses’ obedience, yet in Exodus 16:20, some people disobeyed by keeping manna until morning against God's command.
Exodus 16:20: Notwithstanding they hearkened not unto Moses; but some of them left of it until the morning, and it bred worms, and stank: and Moses was wroth with them.
Contradiction with Exodus 16:27-28
Contradicting with the notion of complete obedience in Exodus 40:16, this verse shows people going out to gather manna on the seventh day contrary to God’s instructions.
Exodus 16:27-28: And it came to pass, [that] there went out [some] of the people on the seventh day for to gather, and they found none.
Contradiction with Numbers 14:1-2
In Exodus 40:16, instructions are followed as commanded, but here, the Israelites rebel against God's command to enter the Promised Land.
Numbers 14:1-2: And all the congregation lifted up their voice, and cried; and the people wept that night.