Corrected entry: Tuatha uses a spell to disempower a witch, and the spell requires "a fresh human heart". Tuatha is an evil witch, so why is the same spell in the The Book of Shadows, a book of good magic? A spell requiring a fresh human heart is obviously not good magic, and the only way an evil spell could appear in the book is if the Charmed Ones themselves were evil, which they are not.
Corrected entry: Tuatha says that there is no such thing as a courage potion, and when the girls search the book of shadows they also say that there is no magical way of giving confidence. But in episode 1-11, 'Feats of Clay', Piper casts a confidence spell on Doug so he will stop breaking everything in the restaurant.
Correction: Given that the confidence spell on Doug backfired and turned him into a conceited ass, they likely discounted that spell right away.
Correction: This is not a mistake, but ties into the exact nature of witchcraft. The craft itself is neither good nor evil, it is neutral. It is the witch using it that decides whether to use it for good or evil. It was included in the Book of Shadows as a reference or in a rare case when a good witch may have no choice to use it, maybe not by killing for a human heart, but obtaining one from a recently deceased person. Tuatha used to be a good witch, but turned evil. The spell may have been in her book when she was good, but she only started using it when she turned evil. It's the intent of the witch in how those are used. There are many spells and potions in the Book of Shadows that cause death or harm, again the intent is how they are used. If the girls had been more advanced in their craft they would have probably anticipated that Tuatha would cast that spell to take away their power.