The emphasis on hidden knowledge and understanding, for one thing.
And you can also see the Gnostic cosmology and narrative in verses like verse 18:
The disciples said to Jesus, "Tell us, how will our end come?" Jesus said, "Have you found the beginning, then, that you are looking for the end? You see, the end will be where the beginning is.
Congratulations to the one who stands at the beginning: that one will know the end and will not taste death."
In Gnosticism, we all originally dwelt in the Pleroma, or the Divine Fullness. But after the fall of Sophia and the Demiurge's creation of the world using sparks and fragments of the light of the Pleroma (i.e. us), we became trapped in the world. And over time, we forgot our divine origins, and you basically have a situation like that of the Matrix, where this false world fashioned by the Demiurge keeps us imprisoned, and we are ignorant to the truth about this world and the true world (the Pleroma) beyond it. In Gnosticism, the goal is to return to the Pleroma, and reunite our divine sparks with the Father.
The idea of our divine sparks becoming entrapped within this material realm fashioned by the Demiurge is clearly seen in verse 29:
Jesus said, "If the flesh came into being because of spirit, that is a marvel, but if spirit came into being because of the body, that is a marvel of marvels. Yet I marvel at how this great wealth has come to dwell in this poverty."
"This great wealth" refers to our spirits, and the divine spark within. "This poverty" refers to our physical bodies, and the physical world which they inhabit.
The Gnostic concept of the Pleroma can be seen in verse 50, exactly as I have described it:
Jesus said, "If they say to you, 'Where have you come from?' say to them, 'We have come from the light, from the place where the light came into being by itself, established [itself], and appeared in their image.'
If they say to you, 'Is it you?' say, 'We are its children, and we are the chosen of the living Father.'
If they ask you, 'What is the evidence of your Father in you?' say to them, 'It is motion and rest.'
The idea that we are ignorant of the truth of this world can be seen in verses 28 and 56:
Jesus said, "I took my stand in the midst of the world, and in flesh I appeared to them. I found them all drunk, and I did not find any of them thirsty. My soul ached for the children of humanity, because they are blind in their hearts and do not see, for they came into the world empty, and they also seek to depart from the world empty. But meanwhile they are drunk. When they shake off their wine, then they will change their ways."
Jesus said, "Whoever has come to know the world has discovered a carcass, and whoever has discovered a carcass, of that person the world is not worthy."
So, though the so-called Gospel of Thomas does contain actual sayings of Jesus that either perfectly or mostly match those found in the actual Gospels, the Gospel of Thomas is not orthodox because of its Gnostic flavor and ideas.