Plot hole: When teenage Prue has run away with the demon, and Phoebe and Piper find her in the park, teenage Prue is 'killed'. Her sisters drive her home to get Leo to heal her, but shouldn't they have just been able to call to Leo to orb to them when Prue was first hurt, and heal her in the park, and save driving back to the Manor and risk Prue dying?
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: 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.
Plot hole: The innocent who gets Piper's powers uses them to freeze Piper and Phoebe. But even though Piper and Phoebe no longer have their unique powers, they are still good witches; they were still able to scry, and we have encountered good witches on the show in the past who had no powers at all. And by the rules of magic within the show, good witches do not freeze.
Plot hole: One of the sisters asks why the familiar doesn't just jump in front of a bus 5 times, another responds with "we're the only ones strong enough to kill him." If they are the only ones strong enough to kill him, then how come two scenes later he falls on a knife during a fight with Phoebe and dies? If a knife can kill him then it doesn't make sense that he seeks out the charmed ones.
Plot hole: According to the family tree viewed in this episode, Penny "Grams" Halliwell was born on 6/23/1937, and her daughter Patty, the Charmed Ones' mother, was born on 4/5/1950. In addition, Patty's father was born in 1930. So, according to this, Penny gave birth to her daughter at age 12, while married to a 20 year old man. That's quite outlandish, to say the least. (00:20:05)
Plot hole: In episode 1-2 ("I've Got You Under My Skin"), Alec buys Phoebe a martini at Quake. but then in episode 5-11 ("The Importance of Being Phoebe"), Cole tells Kaya that Phoebe doesn't drink. Then, in episode 5-17 ("Lucky Charmed"), Jason buys Phoebe a "Martini, dirty" at the end.
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.
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.
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.
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: 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.
Plot hole: Piper mentions that Grams banished the Necromancer "sixty years ago" at Patty's Wiccanning. Grams soon thereafter says that the Necromancer has had "almost seventy years" to regain his strength. However, Patty was born in 1950, and this episode aired on 5/4/03, at which time Patty's Wiccanning could not have been more than 53 years earlier.
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.