Contradiction with Matthew 3:11
This verse says John baptized with water, but implies that Jesus will baptize with the Holy Ghost and fire, not water.
Matthew 3:11: I indeed baptize you with water unto repentance: but he that cometh after me is mightier than I, whose shoes I am not worthy to bear: he shall baptize you with the Holy Ghost, and [with] fire:
Contradiction with John 1:33
States that John the Baptist did not know Jesus initially, which contrasts with the statement in Acts 11:16 about Jesus saying John baptized with water.
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 Acts 2:38
Here, the baptism with the Holy Ghost is tied to the forgiveness of sins, which is not mentioned in Acts 11:16.
Acts 2:38: Then Peter said unto them, Repent, and be baptized every one of you in the name of Jesus Christ for the remission of sins, and ye shall receive the gift of the Holy Ghost.
Contradiction with Acts 8:16
Indicates that people had been baptized in the name of Jesus but had not yet received the Holy Ghost, which contradicts the immediate receipt implied in Acts 11:16.
Acts 8:16: (For as yet he was fallen upon none of them: only they were baptized in the name of the Lord Jesus.)