It didn't quite mesh with Paul's made up version, which is what the church had decided to tell people was the truth. They have spent the last thousand years or so trying to keep it that way. Anything or anyone that didn't agree with their spouted dogma was either destroyed or hidden. I would give my right arm to get into the Catholic archives in Rome. The stuff they have in there would shake the world.
Momo004 is quite correct. Instead of repeating what he correctly said, let me just add one additional aspect. Thomas is not structured like a story, it's basically a collection of sayings attributed to Jesus. When they wanted to coalesce and unite the early church under uniform scripture, especially when there was still much persecution of Christians, they wanted to keep a small number of texts with a cohere t message, and that the gospels will tell a story. A collection of sayings did not fit the mold.