Contradiction with Isaiah 40:3
Contradiction arises in the interpretation of the way prepared, as Matthew 3:3 applies it to John the Baptist and Jesus, while Isaiah 40:3 speaks directly about the coming of the Lord and the restoration of Israel without specifying individuals.
Isaiah 40:3: The voice of him that crieth in the wilderness, Prepare ye the way of the LORD, make straight in the desert a highway for our God.
Contradiction with Malachi 4:5-6
This verse speaks of Elijah coming before the great and dreadful day of the Lord, contradicting Matthew 3:3 where John the Baptist fulfills the prophecy of preparing the way, implying the prophecy of Elijah was fulfilled differently.
Malachi 4:5-6: Behold, I will send you Elijah the prophet before the coming of the great and dreadful day of the LORD: