Their flaw was that the guy who wrote them was an honest-to-god cult leader, who didn't mean the books as fantasy tales but as recruiting tools for his New Age cult. Ultimately, he indirectly caused the death of at least one of his closest followers, and possibly three more [1].
The first book was also basically an instance of academic fraud: "The teachings of Don Juan" was first published as a work of real anthropological research into the mystical practices of Yaqui Indians, but it had nothing to do with them and in any case it was not the result of field work as it was presented. In later books Castaneda clearly tries to retcon this by pointing out that Don Juan's tradition is unique and separate from Yaqui shamanic beliefs. One of his followers, Florinda Donner, also published a made-up anthropology book [2], btw.
After finding all this out it would be really hard for me to read the books today and enjoy them.
Maybe that's overreacting. I've been way more relaxed about the lives of other authors I read; like Lovecraft, for example. I was once called a fascist because I said that Starship Troopers is one of my favourite Sci Fi books. I ignored Heinlein's politics and I only read it as fiction and I still think it's clearly just fiction. The guy who called me a fascist, btw, is a Warhammer 40K player with a Grey Wolves army. Hmph.
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[1] https://en.wikipedia.org/wiki/Taisha_Abelar#Disappearance