Contradiction with Genesis 22:1-2
While 1 Samuel 3:6 describes God calling Samuel, in Genesis 22:1-2, God calls Abraham to test his faith without confusion, unlike the unclear voice Samuel experiences.
Genesis 22:1-2: And it came to pass after these things, that God did tempt Abraham, and said unto him, Abraham: and he said, Behold, [here] I [am]. [Behold...: Heb. Behold me]
Contradiction with 1 Kings 19:12-13
In 1 Samuel 3:6, Samuel hears God calling directly, but in 1 Kings 19:12-13, Elijah experiences God's presence in a gentle whisper, suggesting different modes of divine communication.
1 Kings 19:12-13: And after the earthquake a fire; [but] the LORD [was] not in the fire: and after the fire a still small voice.
Contradiction with John 10:27
1 Samuel 3:6 illustrates Samuel's initial inability to recognize God's voice, whereas John 10:27 speaks of the sheep (followers) knowing and recognizing the shepherd's (God's) voice immediately.
John 10:27: My sheep hear my voice, and I know them, and they follow me: