Wikipedia does a good job of summarizing the heresy, but I want to pull out some source material.
Some of the sayings do attest to the synpotic Gospels, but there is a lot of heresy in there too:
From the top, selected parts of The Gospel of Thomas:
These are the secret sayings that the living Jesus spoke and Didymos Judas Thomas recorded.
1. And he said, "Whoever discovers the interpretation of these sayings will not taste death."
Gnostics were all about "special knowledge." That's where the word comes from: Gnosis - to know. Orthodox Christianity tends to find "secret knowledge" repugnant.
The dead are not alive, and the living will not die. During the days when you ate what is dead, you made it come alive. When you are in the light, what will you do? On the day when you were one, you became two. But when you become two, what will you do?"
This eschataology differs significantly.
- Jesus said to his disciples, "Compare me to something and tell me what I am like."
Simon Peter said to him, "You are like a just messenger."
Matthew said to him, "You are like a wise philosopher."
Thomas said to him, "Teacher, my mouth is utterly unable to say what you are like."
Jesus said, "I am not your teacher. Because you have drunk, you have become intoxicated from the bubbling spring that I have tended."
And he took him, and withdrew, and spoke three sayings to him. When Thomas came back to his friends they asked him, "What did Jesus say to you?"
Thomas said to them, "If I tell you one of the sayings he spoke to me, you will pick up rocks and stone me, and fire will come from the rocks and devour you."
More secret knowledge, and an implication that Jesus is merely a teacher, nothing more.
- Jesus said, "When you see one who was not born of woman, fall on your faces and worship. That one is your Father."
22 ... Jesus said to them, "When you make the two into one, and when you make the inner like the outer and the outer like the inner, and the upper like the lower, and when you make male and female into a single one, so that the male will not be male nor the female be female, when you make eyes in place of an eye, a hand in place of a hand, a foot in place of a foot, an image in place of an image, then you will enter [the kingdom]."
Matter is evil according to gnostics, and the implication here is that matter cannot enter into the kingdom
- "If you do not fast from the world, you will not find the (Father's) kingdom. If you do not observe the sabbath as a sabbath you will not see the Father."
Legalism, and anti-materialism
- 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."
- His disciples said, "When will you appear to us, and when will we see you?"
Jesus said, "When you strip without being ashamed, and you take your clothes and put them under your feet like little children and trample them, then [you] will see the son of the living one and you will not be afraid."
Gnostics were antinomian as a result of their anti-materialism. This would be a kind of that.
- Jesus said, "The Pharisees and the scholars have taken the keys of knowledge and have hidden them. They have not entered nor have they allowed those who want to enter to do so.
More secret knowledge
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.'"
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."
- Jesus said, "I disclose my mysteries to those [who are worthy] of [my] mysteries.
More secret knowledge
Jesus said, "Whoever has come to know the world has discovered the body, and whoever has discovered the body, of that one the world is not worthy."
Jesus said, "Images are visible to people, but the light within them is hidden in the image of the Father's light. He will be disclosed, but his image is hidden by his light."
Jesus said, "When you see your likeness, you are happy. But when you see your images that came into being before you and that neither die nor become visible, how much you will have to bear!"
Jesus said, "How miserable is the body that depends on a body, and how miserable is the soul that depends on these two."
Do you see a pattern here?
Gnostics believe the body is inherently and irredeemably evil. Therefore, it doesn't matter what the body does - only your spirit matters. That is the heart of the antinomian heresy that Gnostics teach.
Beyond this, yes, there is a lot of repetition of the Synoptic Gospels - after all Gnostics thought they were Christians too. But the innovative parts of Thomas are the parts that orthodox Christians either thought "meh" or heresy.
That's why it never made the canon.