Contradiction with Exodus 33:11
God speaks to Moses face-to-face, which contrasts with the indirect method of speaking used for Samuel through a voice at night in 1 Samuel 3:9.
Exodus 33:11: And the LORD spake unto Moses face to face, as a man speaketh unto his friend. And he turned again into the camp: but his servant Joshua, the son of Nun, a young man, departed not out of the tabernacle.
Contradiction with Numbers 12:6-8
God states he speaks clearly to Moses and not in riddles, differing from the way God spoke indirectly to Samuel as suggested in 1 Samuel 3:9.
Numbers 12:6-8: And he said, Hear now my words: If there be a prophet among you, [I] the LORD will make myself known unto him in a vision, [and] will speak unto him in a dream.
Contradiction with John 14:16-17
The presence of the Holy Spirit who communicates directly with believers contrasts with the intermediary role Eli suggests to Samuel in 1 Samuel 3:9.
John 14:16-17: And I will pray the Father, and he shall give you another Comforter, that he may abide with you for ever;
Contradiction with Acts 2:17
The prophecy of God speaking directly to sons and daughters through visions and dreams contrasts with the guidance via Eli's instructions in 1 Samuel 3:9.
Acts 2:17: And it shall come to pass in the last days, saith God, I will pour out of my Spirit upon all flesh: and your sons and your daughters shall prophesy, and your young men shall see visions, and your old men shall dream dreams:
Contradiction with Hebrews 1:1-2
God speaks through His Son in these last days, which differs from the Old Testament approach seen in 1 Samuel 3:9 with guidance through a priest.
Hebrews 1:1-2: God, who at sundry times and in divers manners spake in time past unto the fathers by the prophets,