Contradiction with John 9:31
Jonah 2:1 depicts Jonah praying in distress, while John 9:31 states that God does not listen to sinners, questioning whether Jonah should be heard.
John 9:31: Now we know that God heareth not sinners: but if any man be a worshipper of God, and doeth his will, him he heareth.
Contradiction with Proverbs 28:9
Jonah prays in Jonah 2:1, but Proverbs 28:9 suggests the prayers of those who reject the law are an abomination, potentially contradicting Jonah's disobedience.
Proverbs 28:9: He that turneth away his ear from hearing the law, even his prayer [shall be] abomination.
Contradiction with Isaiah 59:2
Jonah 2:1 describes Jonah's prayer reaching God, yet Isaiah 59:2 implies iniquities could prevent God from hearing.
Isaiah 59:2: But your iniquities have separated between you and your God, and your sins have hid [his] face from you, that he will not hear. [have hid: or, have made him hide]
Contradiction with Jeremiah 14:11-12
While Jonah's prayer in chapter 2 is answered, Jeremiah 14:11-12 suggests that God may refuse to listen to certain prayers.
Jeremiah 14:11-12: Then said the LORD unto me, Pray not for this people for [their] good.
Contradiction with James 4:3
Jonah’s successful prayer in Jonah 2:1 contrasts with James 4:3, which says prayers asked amiss won't be granted.
James 4:3: Ye ask, and receive not, because ye ask amiss, that ye may consume [it] upon your lusts. [lusts: or, pleasures]