Valhalley of the Dolls (1) - S6-E1
Plot hole: Phoebe becomes an empath. But in Primrose Empath (S3:E6) Leo tells the sisters an empath is a mortal who has died and come back as an empath, so it wouldn't be a progression of a witch's powers like it is in this episode. Plus Phoebe isn't dead.
Suggested correction: There is a difference between an Empath and the power of Empathy. A true Empath is a mortal that has died and been reincarnated and they are a separate race of magical beings. But other beings, such as witches, can have the power of empathy. It does get confusing because they refer to a witch with empathy as an empath, but that doesn't mean they are true empaths. In addition, Phoebe developed her empathy powers in her 20's as one of her first powers and her power of empathy is the strongest of any being.
And where is this stated anywhere in the 8 seasons of the show?
The Power of Three Blondes - S6-E4
Plot hole: Paige sees Margo leading the labor rally at the citrus factory, and then is stopped by a security guard. In the next scene, Margo and her sisters are entering the manor, and then after that Paige is thrown out of the factory. But how did Margo get from the factory to the manor before Paige was thrown out, when she was in the middle of the rally?
Plot hole: When Gith takes the potion from Chris, he ends up stomping on it and shattering the potion bottle - making contact with the potion. We've seen that potions don't have to be thrown by someone who's even a witch for them to work (like when Cole's powers were stripped etc) so why on earth would he do this? And how did it not vanquish him? There are other ways he could have gotten rid of the potion that didn't involve a way that really should have vanquished him.
Plot hole: It's shown with the spell that the Halliwells leave for Chris in the attic that if something happens in the past, the future will immediately reflect that change. Chris had changed so much in the past that there should have been at least one thing different that mildly surprised him, even if he was careful to not give too much information to the sisters about the future.
Witchstock - S6-E11
Plot hole: In the opening scene, Chris directs Piper and Phoebe on how to vanquish the amorphous demon. He says that it will attack "fast and hard" as soon as it senses Phoebe's magic when she levitates. But Chris had orbed out of the warehouse and back in, and the demon didn't react to the magic. Later in the episode, it is specifically attracted to a use of orbing, several times.
Witchstock - S6-E11
Plot hole: This episode takes place in 1967, and Penny (Grams) is married to a man named Allen Halliwell who dies in the episode. Allen is supposed to be Penny's "first husband," Patty's father and the Charmed Ones' grandfather. But it was previously established that Patty's father was named Jack, and he died in 1964. Also they hint that Patty is still little but we know she was born in 1950 so she would be 17.
Witchstock - S6-E11
Plot hole: After Paige changes the past, the ghost of Grams changes from a no-nonsense demon-hunter into a pacifist hippie. So, apparently, we are now in an alternate timeline where Grams never became assertive, and stayed a hippie all her life. The episode went to great lengths to establish that if Grams had stayed a hippie, she and the Charmed Ones would have all died young. But the ghost of Grams was still middle-aged, instead of decades younger, and Wyatt and Chris were still there, but they wouldn't have been if their mother Piper had died as a child.
Plot hole: Rick is menacing Phoebe with a gun near the end of the episode. Why doesn't Paige orb the gun away from him? In fact, why did Phoebe make Piper stay upstairs? Piper could have frozen Rick, and Paige could have orbed him back to the prison. There were several obvious ways to resolve this situation that would not have caused Rick's death.
Witch Wars - S6-E21
Plot hole: In the beginning of the episode the opening screen row Witch Wars has images of the witch Paige saved before the event actually occurred.