Contradiction with Exodus 14:21
While Jonah 1:4 describes God stirring up the sea, Exodus 14:21 shows God calming the sea to create a dry path.
Exodus 14:21: And Moses stretched out his hand over the sea; and the LORD caused the sea to go [back] by a strong east wind all that night, and made the sea dry [land], and the waters were divided.
Contradiction with Psalm 89:9
Jonah 1:4 describes God's power in causing a tempest, whereas Psalm 89:9 speaks of God's power in calming the sea.
Psalm 89:9: Thou rulest the raging of the sea: when the waves thereof arise, thou stillest them.
Contradiction with Mark 4:39
Jonah 1:4 illustrates God causing a storm, while in Mark 4:39, Jesus, who is God in Christian belief, calms the storm.
Mark 4:39: And he arose, and rebuked the wind, and said unto the sea, Peace, be still. And the wind ceased, and there was a great calm.
Contradiction with Matthew 8:26
Jonah 1:4 involves God's agency in raising a storm, whereas in Matthew 8:26, Jesus rebukes the winds and the sea to bring a calm.
Matthew 8:26: And he saith unto them, Why are ye fearful, O ye of little faith? Then he arose, and rebuked the winds and the sea; and there was a great calm.
Contradiction with Psalm 107:29
Jonah 1:4 shows God unsettling the sea, while Psalm 107:29 depicts Him bringing peace to the tumultuous waters.
Psalm 107:29: He maketh the storm a calm, so that the waves thereof are still.
Contradiction with John 6:19-21
Jonah 1:4 tells of divine intervention to disturb the sea, but in John 6:19-21, Jesus calms the conditions to bring safety.
John 6:19-21: So when they had rowed about five and twenty or thirty furlongs, they see Jesus walking on the sea, and drawing nigh unto the ship: and they were afraid.