The Kids Are Alright (1) - S6-E1
Plot hole: When Joey walks into her class and sits down, her cell phone rings and her Professor answers it. As he listens to Audrey on the other end, he says very quickly that he got the message. But when he relays the entire message to Joey after he hangs up, the message is much longer. There is no way he could have possibly gotten that long a message in the very short time he was talking to Audrey and said 'he got it'.
Everything Put Together Falls Apart - S6-E9
Plot hole: When Pacey first finds Emma in the bathroom cleaning the toilet, she makes a point of mentioning that 'she has band practice in an hour'. But right after they 'strike a deal' and Pacey agrees to her terms for the party, Emma suddenly announces that 'she is off to band practice'. Only a few minutes have passed, so it seems strange Emma would suddenly be going to a band practice that doesn't actually start for another hour.
Rock Bottom - S6-E13
Plot hole: The episode starts with Joey frantically trying to get to class, and printing out a paper she obviously has to turn in for that class. But then Eddie suddenly shows up at her door, and after hearing from Audrey's Mom, Joey suddenly decides to ditch school for a few days to drive across Country to LA. This doesn't sound like something the studious Joey would do, especially with her Scholarship in jeapordy from her failing grade on the midterm. Why would she take a few days off from school, in the middle of the week with classes and further jeopardize her academic standing at a very expensive University? It wasn't Spring Break yet either, that comes in a later episode. Even though Joey would have to fly back from LA, it would still take them at least 2 or 3 days to drive from Boston to LA. Would Joey really just take off like that and ditch all her academic responsibilities considering how serious she is about her education? Doesn't seem reasonable for her character.
Plot hole: When Pacey and Joey get locked in the Big K-Mart, they run to the front doors and start banging on them and yelling at the guard. The guard, who is in the parking lot turns back towards his car and faces directly towards Joey and Pacey in the front windows. They aren't that far from the guard's car, and he was looking directly towards them. There is no way the guard would not have noticed two full-grown adults standing in the front glass doors pounding their hands on the glass and yelling at him.
Plot hole: When Pacey and Joey are in the break room, waiting for the police to call them back, they start arguing. The phone suddenly rings, and Joey asks Pacey not to answer it in order to finish their conversation. But this doesn't make logical sense; considering their desperate circumstances (being locked in the store all night) and how hard they tried to get hold of law enforcement to help them get out, there is no way Joey would not want to answer such a critical phone call. It may have been their only chance to communicate with help.
Love Bites - S6-E18
Plot hole: At the end of the episode, Joey takes a taxi from Boston to Eddie's house in Worcestor. As she walks up to the front door, the cab leaves. Eddie has no idea Joey is coming, and she has no way to return to Boston without using a cab or asking Eddie for a ride. But she doesn't even know yet if Eddie is home, and whether he would offer to drive her home. Seems illogical for Joey to dismiss the cab without asking the cab driver to wait a few moments while she sees if Eddie is home, and if he would be willing to drive her back to Boston. Otherwise, she would have to ask his parents to use the phone to call another cab. (00:38:45)
Goodbye, Yellow Brick Road - S6-E21
Plot hole: In the beginning of the episode, Joey and Audrey are talking in their dorm room. Audrey makes a comment that "Our time in this particular room is over". They have been in the same dorm room (27) for two years now, their Freshman and Sophomore years at Worthington. They still have 2 more years to go. What would make Audrey think that they would suddenly have to change dorm rooms when they've had the same room the entire time? Or that they wouldn't still be roommates the next academic year at Worthington? Audrey is staying to take Summer School classes so she doesn't have to leave the University. (00:08:40)
Joey Potter and the Capeside Redemption - S6-E22
Plot hole: When Jen and Grams are talking on the porch, Dawson walks up to talk to them. They ask him if their cab has arrived, and he says no, but they are in his shot. They then choose that time to say goodbye to Dawson, which turns into a group 'goodbye' with everyone that lasts several minutes. Meanwhile, the cab has arrived, and when they are finished saying goodbye, Grams, Jack and Jen walk to the cab and get in to leave for NYC. But what happened to all their luggage for the trip? How did it get in the cab? They went straight from saying goodbye, into the cab without stopping to carry their luggage to the car.
Joey Potter and the Capeside Redemption - S6-E22
Plot hole: During this entire episode, Audrey is helping to film Dawson's movie by playing the role of Ms. Jacobs. We already know that Audrey is in the midst of Summer School at Worthington, but she is apparently staying down in Capeside during the entire time of filming. Audrey doesn't own a car in Boston, and it would be very difficult for her to commute every day to school and back. So why would she suddenly take off several days to do Dawson's movie when she is in the middle of Summer School classes? She mentions how boring the classes are, implying they are still going when she decides to do the film. Given that her academic standing is in jeapordy from missing almost an entire semester previously, it doesn't seem likely she would ditch her classes during the Summer to take off and film a movie.
All Good Things... (1) - S6-E23
Plot hole: When Jen and Jack are talking at the B&B, he picks up the bottle of pills from Jen's purse and asks her about them. She lies, telling him they are pills for Grams when in reality they are Jen's medication. But Jack is examining the label closely, and wouldn't he see pretty easily that Jen's name was listed instead of Grams? He had plenty of time to read the entire label. (00:28:40)
All Good Things... (1) - S6-E23
Plot hole: Dawson is in his bedroom, and hears a noise outside his window. He panics, and picks up his laptop to use as a 'weapon' if necessary, while approaching the window. This doesn't seem logical; because for one thing he knows Joey is in town and she has been coming in through that window for years, and wouldn't he think of that first? Also-highly unlikely Dawson would actually use a very expensive Apple laptop as a weapon when it could be damaged, and he relies on it extensively for his work as a Writer/Producer. (00:30:55)
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.