Contradiction with Mark 16:14
This verse mentions Jesus appearing to the eleven disciples, including Thomas, which contradicts John 20:24 where Thomas is said to not be present.
Mark 16:14: Afterward he appeared unto the eleven as they sat at meat, and upbraided them with their unbelief and hardness of heart, because they believed not them which had seen him after he was risen. [at meat: or, together]
Contradiction with Matthew 28:16
This verse implies that all the disciples went to Galilee to meet Jesus, which contradicts John 20:24 suggesting Thomas was absent during an initial appearance in Jerusalem.
Matthew 28:16: Then the eleven disciples went away into Galilee, into a mountain where Jesus had appointed them.
Contradiction with Luke 24:36
This verse describes Jesus appearing to "them," presumably all the disciples, contradicting John 20:24 indicating that Thomas was not present.
Luke 24:36: And as they thus spake, Jesus himself stood in the midst of them, and saith unto them, Peace [be] unto you.