Plot hole: When everyone first shows up at the Airport, it's daytime and not too late. Joey then works an entire shift at the Capeside Yacht Club, probably through the dinner rush until later that night. When Joey and Pacey are talking on the dock after she is through working, it's late at night. They suddenly decide to rush to the Airport where they assume everyone is still waiting for their flights. Being as this must be several hours later since they all met at the Airport, would everyone's flights really be delayed that long? (00:30:05)
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.
Downtown Crossing (2) - S5-E15
Plot hole: When Joey suddenly regains consciousness in the ER, she is sitting upright on the end of a hospital bed or gurney. But this doesn't make logical sense, because if she were really unconscious she would be laying down. Yet it's made very clear in that shot, that she is opening her eyes for the first time after fainting and being unconscious.
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.
Plot hole: During this ending scene, Joey runs frantically to find Pacey and asks to go with him on his sailing trip all Summer. She is carrying absolutely nothing with her, not even a purse or wallet. Her pockets are completely flat, and she doesn't even appear to have ID. Joey's lack of luggage or clothing is explained in her dialogue, as she jokes about the next change of clothing. She probably assumed she could buy what she needed along the way, and was in a hurry not to miss Pacey's departure. But it doesn't seem logical that she would take off for an entire Summer without any type of purse, wallet, money, credit cards, ID, etc. as she would have no way to pay for anything. She would also need her ID in order to work the odd jobs she mentions in Season 4. (00:39:10)
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.
Plot hole: During Season 4, at Graduation, Andy informs Jack that she is 'deferring Harvard for a year' and going back to Italy instead, as she is happy there. Therefore, it makes logical sense that we never see Andy's character in all of Season 5, when all the other major characters ended up in Boston together. But it doesn't explain Season 6, when Andy should have been back in Boston attending Harvard University. It isn't likely she would have jeopardised her education and deferred a prestigious college like Harvard for more than a year (they probably wouldn't allow it); and if she was, in fact attending Harvard in Boston during Season 6 and she was such good friends with everyone, surely she would have hung out with them at times! Everyone else did. It doesn't make logical sense that Andy was attending college in Boston along with everyone else that year, but they never saw her at all. And they never explained her absence at all in the scripts. Plus the fact that in the Series Finale, she is at Mass. General in Boston furthering her medical training; implies she did indeed attend Harvard for her undergraduate, Pre-Med education.
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.
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)
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.
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)
Escape from Witch Island - S3-E7
Plot hole: When Dawson, Joey, Jen and Pacey are stuck on Witch Island after dark-they are suddenly shown using strong flashlights to see their way. But they had never originally intended to be on Witch Island after dark, which was made clear when someone suggested leaving because 'it was starting to get dark'. They were only carrying light daypacks for their day trip, and Pacey even joked about how no-one had bothered packing any snacks. Therefore since no-one intended to be on the Island after dark, and they packed very light day packs without even food, why would they suddenly be carrying large flashlights? It's unlikely they would have bought them at the Witch Island Gift Store, as it wasn't shown and no-one seemed to pay for anything from there.
Answer: It's only explained once in the series. Jack says to Andie "I tried to start kindergarten without you", meaning Andie was smart enough to start school early.