Plot hole: Piper is initially skeptical at Phoebe's theory that the Evil Enchantress could be Paige in a past life, because Paige lacks the Enchantress' ability to summon the elements. However, Piper knows that in Phoebe's past life she had a pyrokinetic power, which she does not have in the present.
Plot hole: According to Paige's "fairy tale" the witch ends up with the prince. If this is really a past life, the sorceress ended up with the prince in the Middle Ages. So why do they have to fix it? Everything was just going the way it did according to her fairy tale, and good magic was obviously still present in the world.
Plot hole: Phoebe and Piper seem surprised at the fact that a white-lighter can impregnate someone, because they are dead. Piper says "how does a white-lighter get somebody knocked up?", but when she went to the future she saw herself with Leo's baby, and Leo told her that he hadn't clipped his wings.
Plot hole: In this episode Cole says "upper level demons have a human form and they bleed red, not green", but when Cole told Phoebe he was half human he said "how else could I bleed red, even in my demonic form".
Plot hole: After Cole explains he might not be able to regain control after embracing his demonic half, he tells Phoebe she should have the Belthazor vanquish potion ready just in case. But in "Look Who's Barking", Piper tried using that potion on Cole and it didn't work because he had himself magically protected from it.
Plot hole: Phoebe says Piper and Prue were able to defeat Shax without the power of three and Piper's response is it was because "Prue was the strongest." Piper would have no recollection of this event as Tempus reversed time bringing Piper back from the dead in the timeline that she was shot in. The time reversal affected everyone's memory except Phoebe, Leo and Cole who were in the Underworld.
Plot hole: Cole explains that the demonic power is driving Karen mad because she is human. Cole later has Paige infected with one to drive her mad. This doesn't make sense since Paige is doubly not human, and shouldn't be driven mad. In fact the Charmed Ones have had demonic powers before and were not driven mad, but instead turned evil.