Contradiction with John 1:21
John denies being Elijah when questioned, while Matthew 17:12 implies John the Baptist fulfilled that role.
John 1:21: And they asked him, What then? Art thou Elias? And he saith, I am not. Art thou that prophet? And he answered, No. [that prophet: or, a prophet?]
Contradiction with Malachi 4:5
Malachi predicts Elijah will come before the great and dreadful day of the Lord, but Matthew 17:12 refers to John the Baptist as Elijah who has already come.
Malachi 4:5: Behold, I will send you Elijah the prophet before the coming of the great and dreadful day of the LORD:
Contradiction with Matthew 11:14
This verse suggests belief in John as Elijah is conditional and subject to acceptance, whereas Matthew 17:12 states it more as a fulfilled fact.
Matthew 11:14: And if ye will receive [it], this is Elias, which was for to come.