Yes but no. Jeanne’s parents killed their dog because they believe it killed baby Jeanne. They discover this wasn’t the case and venerate the dog (Gwenforte) as a saint. The dog later comes back to life, and is alive at the end of the book.
A donkey’s leg is ripped off, but it is said that the donkey does not feel any pain from this, and it reattaches later. A dog is killed in the beginning, but comes back to life. Someone tries and fails to kill her again.
I can’t remember if there’s any tooth injury in the text, but the Jongleur is shown to be missing a tooth in one of the illustrations. It’s not graphic at all.
Not completely nude, but William fights the Fiends in a forest while in his underwear. He later washes off their blood from his upper body and the other two children see.
Jacob’s parents are heavily implied to have died in a village fire.
Also
SPOILERS: Michelangelo is burned alive and the children believe him to be dead. At the very end of the book, it is revealed he is alive- and likely did not feel any pain.
No characters are actually tortured during the book, but chapter 15 has descriptions of saints being tortured. It’s a mostly lighthearted conversation. Also, considering the title of the book, and knowing what an Inquisitor is, there are themes of torture.
No characters are confirmed to be autistic, and it was not a diagnosis in medieval times, but there could be similarly triggering content due to subtext
The main conflict in the second half of the story is the king of France trying to burn every Talmud (Jewish holy book)
SPOILERS
He succeeds and at first it is believed that all of them have been destroyed, but there turn out to be a few left.
Not by the strictest definition, but in the broader meaning of manipulation: Jeanne in the first couple chapters, and all three children by the Abbot in chapter 14
In the sense of the storytelling being non-linear and non-traditional, and that fact being joked about by the characters. The story is told by characters sitting around a table at an inn, and all the characters have different perspectives. We only learn about the main narrator, and how he is involved in the story, near the end.