Contradiction with Genesis 15:13
This verse states that Israel would be afflicted for 400 years, while Exodus 3:9 suggests immediate divine intervention.
Genesis 15:13: And he said unto Abram, Know of a surety that thy seed shall be a stranger in a land [that is] not theirs, and shall serve them; and they shall afflict them four hundred years;
Contradiction with Exodus 2:23
Suggests the Israelites' cries for help had been going on for a long period, possibly without a direct response until Exodus 3:9.
Exodus 2:23: And it came to pass in process of time, that the king of Egypt died: and the children of Israel sighed by reason of the bondage, and they cried, and their cry came up unto God by reason of the bondage.
Contradiction with Exodus 4:31
Implies the Israelites believed God had already seen their affliction, seemingly contradicting the timing of Exodus 3:9 as God's initial notice.
Exodus 4:31: And the people believed: and when they heard that the LORD had visited the children of Israel, and that he had looked upon their affliction, then they bowed their heads and worshipped.