Contradiction with Genesis 18:20-21
Mark 6:46 describes Jesus praying alone, while Genesis 18:20-21 has God discussing plans with Abraham, implying the Godhead engages others.
Genesis 18:20-21: And the LORD said, Because the cry of Sodom and Gomorrah is great, and because their sin is very grievous;
Contradiction with Matthew 6:5
Mark 6:46 depicts solitary prayer, whereas Matthew 6:5 warns against praying publicly for attention.
Matthew 6:5: And when thou prayest, thou shalt not be as the hypocrites [are]: for they love to pray standing in the synagogues and in the corners of the streets, that they may be seen of men. Verily I say unto you, They have their reward.
Contradiction with Luke 9:28
Mark 6:46 shows Jesus praying alone, but Luke 9:28 highlights Jesus taking others to pray.
Luke 9:28: And it came to pass about an eight days after these sayings, he took Peter and John and James, and went up into a mountain to pray. [sayings: or, things]