Contradiction with John 7:48
Whereas Matthew 21:45 suggests the Pharisees understand Jesus' parables, John 7:48 suggests that those knowledgeable in the law do not believe in Jesus.
John 7:48: Have any of the rulers or of the Pharisees believed on him?
Contradiction with Luke 8:10
While Matthew 21:45 shows the Pharisees understanding Jesus is speaking about them, Luke 8:10 suggests that parables are meant to obscure understanding, not reveal it, to those outside of the disciples.
Luke 8:10: And he said, Unto you it is given to know the mysteries of the kingdom of God: but to others in parables; that seeing they might not see, and hearing they might not understand.
Contradiction with John 12:37-40
Matthew 21:45 indicates that the Pharisees understand the implications of Jesus' words about them, but John 12:37-40 suggests that they are blinded and cannot understand or believe.
John 12:37-40: But though he had done so many miracles before them, yet they believed not on him:
Contradiction with Acts 28:26-27
While Matthew 21:45 shows awareness among the Pharisees, Acts 28:26-27 reflects the condition of the audience having closed eyes and ears, unable to see or hear truth.
Acts 28:26-27: Saying, Go unto this people, and say, Hearing ye shall hear, and shall not understand; and seeing ye shall see, and not perceive:
Contradiction with 1 Corinthians 2:14
Matthew 21:45 depicts the Pharisees recognizing themselves in Jesus' parables, but 1 Corinthians 2:14 argues that spiritual truths are considered foolish and not understood by the natural man.
1 Corinthians 2:14: But the natural man receiveth not the things of the Spirit of God: for they are foolishness unto him: neither can he know [them], because they are spiritually discerned.