Plot hole: When Pacey and Andie are talking at the Senior Party, she excitedly mentions that he will be in the Caribbean that Summer. Pacey says that Andie would be in Florence, Italy. This doesn't make sense, because at that point in the episode, none of Andie's friends knew she was returning to stay in Italy. In fact, later during the graduation ceremony, Andie is talking to her brother Jack. He is the first person she tells the news to, and even says, "I haven't told anyone else this". So how would Pacey know the night before that Andie had decided to stay in Italy longer? (00:30:45 - 00:37:25)
Two Gentlemen of Capeside - S4-E3
Plot hole: When the storm hits the Capeside Yacht Club, Andie takes charge and tells Mrs. Valentine to write down two phone numbers and call Dawson's parents, and Jen's grandmother. But she forgets completely about Joey and Pacey, both of whom are in harm's way, especially Pacey. Seems illogical she would have Mrs. Valentine call about two of the people out at sea, but not the other two. Joey's family and Pacey's family would also be concerned.
Coming Home - S4-E1
Plot hole: Dawson mentions to everyone on the beach, that he and Jack have to go paint their 'last home of the season', implying they have been earning money by painting homes around Capeside. However, when Dawson and Jack stop by the hardware store to get supplies, Dawson picks out a metal handle for the paint rollers. Paint and new rollers makes sense, but if they have indeed painted other houses that Summer, he probably wouldn't need a more substantial piece of equipment as the heavy duty metal paint roller handle. He would already have one.
Two Gentlemen of Capeside - S4-E3
Plot hole: While out at sea, Jen and Pacey get slammed by the storm. So Pacey decides to take shelter at a small cove that he and Dawson had once used to wait out a storm. Pacey and Jen make it safely to the cove, and wait on the boat in fear of being capsized or drowning. If they are in a cove, and close to shore-why wouldn't they go on land to wait out the storm where they would be safer than in a boat that could be capsized or flooded? They could have probably swam a few feet to get to the shore, since they were already in a small cove that was near land. When Pacey was steering the boat into the cove; there was a noticable man-made jetty they were very close to, so obviously they were within close range of solid land.
Plot hole: During the Leery's Christmas party, Jen asks Jack which colleges he applied to in her name. He replies: Bard, Brown, Columbia, Emerson, Sarah Lawrence, and BU (Boston University). But later in this season, Jen goes to visit NYC because she was accepted into the University of New York. How could she have been accepted there when she never applied? Jack didn't apply for her there, and she didn't fill out any college applications herself.
Falling Down - S4-E2
Plot hole: When Dawson goes over to Joey's house to talk to her about Pacey's school problems, he mentions that Pacey had missed that entire day of school. Joey apparently didn't know this, as she is surprised at the news. Since Joey and Pacey are closely involved - wouldn't she have noticed his absence at school that day already? Surely she would have noticed Pacey missing for an entire day of school.
Falling Down - S4-E2
Plot hole: Mrs. Valentine almost fires Joey, after discovering that she lied about knowing the Owens. Drue steps in and saves Joey's job by claiming he did see the Owen boy. But Joey keeps her job throughout the rest of that season. Since the Owens were said to be in Paris only until the 1st of the year - wouldn't Mrs. Valentine have found that Joey lied about knowing them as soon as they returned to Capeside? Surely Mrs. Valentine would have mentioned Joey to the Owens; thinking she was their good friend, and because she was new on staff at the Country Club they were members of the board for. And once she found out Joey had indeed lied, why did she not fire her at that point?
Coming Home - S4-E1
Plot hole: Dawson and Jen are in a small 'darkroom', developing photos and speaking at a normal level. This darkroom is located just behind the main stairs, and very close to the living room where Dawson's parents are 'getting busy'. Therefore, the parents normally would have heard their voices so close to them, and known they were in the house and not been so surprised by them.
Plot hole: After Drue has spent the night at Jen's house, Grams explains to Jen that she had a nice talk with Drue right after Jen left for school. But this doesn't make sense, because why would Jen have to be at school a certain time, and Drue not go to school at the same time or at all? His attendance at school would have been required as well.
Coming Home - S4-E1
Plot hole: This scene reveals that Joey has brought Dawson a special gift from her sailing trip with Pacey. It's a brick from the foundation of Ernest Hemingway's home in the Florida Keys, symbolic to 'build the foundation of a friendship' between her and Dawson. In reality, it's highly unlikely that anyone would have allowed Joey to damage a foundation wall by prying out a large-sized brick; and steal it from the premises of a famous, historic home and landmark. (00:36:15)
Admissions - S4-E17
Plot hole: When Pacey and Joey are unloading the groceries from the car for her party, Pacey makes a remark that he has to go to Joey's garage to get a dolly to haul in the charcoal. But Joey's house doesn't have a garage. During the entire series; there has never been a visible garage on their property, and the large blue truck is always parked out front in the open.
Plot hole: During the 4th act of this episode, Dawson and Joey spend an evening together as friends. When they are walking out of the coffee shop, they suddenly laugh and switch their coffee cups as if they had each others. This doesn't make logical sense, as they wouldn't know they had the wrong coffees without tasting them first, and if they had tasted them already inside the shop or knew they had the wrong coffees, they probably would have switched the cups then without waiting until they got outside. And usually the coffee is handed to the individual who ordered it, so they wouldn't be switched.
Eastern Standard Time - S4-E18
Plot hole: When Jen introduces Joey to her father in his office, she calls her "Joey Potter from Capeside". But later when they are at dinner, Jen's father suddenly refers to Joey as "Josephine" which seems strange as he wasn't told that was her legal name, and only those who know her well would know that. Joey is not necessarily a nickname only for Josephine, so it wasn't just a logical deduction.
Plot hole: At the end of the episode, when Pacey and Joey finally sleep together, there is a moment before when they are both standing in front of the mirror talking. To the right of the mirror, there is a large window looking directly into the bedroom they are standing in. The curtains are pushed back, and you can see the outside through the window. Pacey and Joey make their way slowly towards the bed, making it clear they have one thing in mind. They don't seem to notice the window which would give full view to their bedroom and bed, and neither of them makes any attempt to close the curtains. Noone seems to care that anyone walking by would be able to look directly in on them while they are 'busy'. (00:39:25)
Plot hole: When Pacey and Joey run into Jen and Jack outside the restaurants, Jack suggests they all go to the pizza place near them. Joey and Pacey agree, and it is implied that all four of them are going to the same place to eat dinner together. But the next shot of inside the pizza restaurant only shows Joey and Pacey seated at a large table with Drue, Anna and the other guys. Jen and Jack are nowhere in sight. It isn't likely Jen and Jack wouldn't be seated with or near Pacey and Joey for dinner, since they suggested they all go there to eat.
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.