Contradiction with Genesis 6:13
God directly communicates His intentions to Noah, just as He does to Jonah, which is not a contradiction but a similarity.
Genesis 6:13: And God said unto Noah, The end of all flesh is come before me; for the earth is filled with violence through them; and, behold, I will destroy them with the earth. [with the earth: or, from the earth]
Contradiction with Numbers 23:19
This verse suggests God does not change His mind, yet in Jonah 1, God's command appears to be followed by a change of events later.
Numbers 23:19: God [is] not a man, that he should lie; neither the son of man, that he should repent: hath he said, and shall he not do [it]? or hath he spoken, and shall he not make it good?
Contradiction with Ezekiel 18:21
It indicates repentance can lead to God relenting from judgment, paralleling Jonah's message to Nineveh but not directly contradicting Jonah 1:1.
Ezekiel 18:21: But if the wicked will turn from all his sins that he hath committed, and keep all my statutes, and do that which is lawful and right, he shall surely live, he shall not die.