Contradiction with Mark 3:17
This verse refers to James and John as "sons of thunder," not specifying any relation to Zebedee, whereas John 21:2 identifies them as "sons of Zebedee."
Mark 3:17: And James the [son] of Zebedee, and John the brother of James; and he surnamed them Boanerges, which is, The sons of thunder:
Contradiction with Matthew 4:21
This verse states that James and John were with their father Zebedee mending nets, suggesting that they never left Galilee, whereas John 21:2 places them elsewhere after the resurrection.
Matthew 4:21: And going on from thence, he saw other two brethren, James [the son] of Zebedee, and John his brother, in a ship with Zebedee their father, mending their nets; and he called them.
Contradiction with Luke 5:10
This verse implies the partnership of James, John, and Simon Peter in fishing earlier in the narrative, contrasting the later rejoining of Simon Peter by these disciples as depicted in John 21:2 without mention of the same partnership structure.
Luke 5:10: And so [was] also James, and John, the sons of Zebedee, which were partners with Simon. And Jesus said unto Simon, Fear not; from henceforth thou shalt catch men.