Job 38:1–18: Does God Call Questioning Him Sin?
Job 38 does not treat every question put to God as sin. God answers Job's speech by showing up in the whirlwind and asking who laid the earth's foundations, and the point is that the creature is not the auditor of the Creator.
Job 13:3: Is It a Sin to Question God?
Job 13:3 records a suffering man saying he wants to speak with the Almighty and reason with God. The verse treats that desire as honest speech, not as sin, which reframes what the Bible calls rebellion.
Habakkuk's Raw Questions to God
Habakkuk asks God hard questions about violence and unanswered justice, and the book presents that speech as revelation rather than rebellion. The passage answers the fear of questioning God by showing a faithful man who asks why and is answered rather than condemned.