Contradiction with John 1:33
This verse states that John the Baptist did not know Jesus beforehand, while Matthew 3:13 implies a prior recognition as John attempts to deter Jesus from baptism, indicating he already knew who Jesus was.
John 1:33: And I knew him not: but he that sent me to baptize with water, the same said unto me, Upon whom thou shalt see the Spirit descending, and remaining on him, the same is he which baptizeth with the Holy Ghost.
Contradiction with Matthew 11:11
This verse suggests the greatness of John the Baptist, yet in Matthew 3:13, he submits to baptizing Jesus, which may seem contradictory to his own significant prophetic role.
Matthew 11:11: Verily I say unto you, Among them that are born of women there hath not risen a greater than John the Baptist: notwithstanding he that is least in the kingdom of heaven is greater than he.