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.
Suggested correction: They all are human, just not mortals.
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.
Suggested correction: This is not a correction, more of an observation that goes with this plot hole. In season 2 episode 14 'Pardon My Past' Leo explains to the sisters that Phoebe had her active powers taken away, because her past self had used them for evil, but yet the Enchantress does the same with her powers, and Paige still has active powers. It took two years for Phoebe fighting as a good witch to actually gain an active power again, and then it was only levitating. Becoming an empath took seven years. So that doesn't really make sense that Phoebe would be punished for her past self actions and Paige was not.
Possibly Paige had past lives in between the one we saw and the present one. So she could have already atoned for the evil past life in another past life.
Also Paige's active power comes from her Whitelighter side not her witch side, she doesn't have any active witch powers.
Paige's active power comes from her whitelighter heritage, so like Chris and Wyatt, she doesn't have an active witch power, so this active power has nothing to do with her Wiccan heritage and past life as the enchantress.
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: Leo suggests to Piper that they use their magic to scare Wyke into a confession. In Ex Libris (Season 2) it is established that they can't/shouldn't use their powers to punish the guilty - even if it means saving/helping an innocent. There's no way Leo would suggest such an immoral course of action.
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. (00:46:25)
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. (00:27:15)
Plot hole: When Yen lo enters the manor in the attic. Where did the water on the floor he comes through come from? Windows were closed, no visible leak, and the sister took precautions to make sure there was no water in the house. Also after he attacks and gets the dragon blade, he exits the house through the sink filled with water. Piper had already said to make sure there was no surfaces of water in the house and had Phoebe and Paige shut the water main off.
Suggested correction: There is a previous scene that shows a visible leak in the windows and an obvious puddle of water on the floor of the attic. This is the same puddle they later enter limbo through. As for the sink, Phoebe (in Paige's body) explains that she had been soaking potion pots and forgot to drain the sink. Turning off the valve wouldn't dissipate water that is already in the sink.
Plot hole: Paige is able to use the enchantress' powers, but in "Pardon My Past", Phoebe can't use her past life's fire throwing power and Leo tells her it's because her past life misused it so she lost it. The enchantress misused her powers so Paige should not be able to use them.