Plot hole: At the beginning of the episode, when Joey and Pacey are kissing in the boathouse on the dock; he lifts her up and puts her on a counter right in front of a window. This window appears to look directly out over the nearby boats and dock, meaning they would have been in full view of all their friends waiting to christen Pacey's boat. Not very logical to be kissing on the sly, right in front of a window where everyone could see them.
Continuity mistake: At the end of the day, Joey and Dawson are laying on his bed talking. When Joey asks Dawson how he would describe his film, there is a close-up of Joey looking directly at Dawson, who is to her left. The next shot, as Dawson answers, Joey is suddenly staring straight up and not looking at Dawson. Then in the next shot, Joey is again looking back at Dawson to her left. The transitions are too fast for her to have actually moved her head. (00:34:10)
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.
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.
Factual error: Towards the end of the episode when Joey and Dawson are arguing about their relationship, Joey makes a statement that "Dawson bought the Champagne" referring to their romantic time on the movie set earlier that evening. However, when they were having that drink on the porch of 'Dawson's House' on the movie set; Dawson explained to Joey that the Champagne was from a free gift basket, one of many given to Directors before they start production on a new film. Therefore, Dawson never bought the Champagne, he simply stole it from the gift basket. (00:36:45)
Continuity mistake: During the beginning intro monologue, Jen is shown seated between her parents on a couch. The two actors portraying her parents are only shown from the back, but they appear to be different people than the original actors who portrayed them. The father, especially has different hair and wears glasses. (00:01:40)
Audio problem: During the narrative for the Season Finale, second half, Paul Stupin the Executive Producer is talking about Joey and Pacey's romance in the show. He mentions that they went on an "epic journey on a sailboat all over the world." He's a bit mistaken; as when Joey and Pacey went sailing at the end of Season 3, they sailed from Massachussetts down the Eastern Coast to Florida and back again. It was hardly "all over the world". (01:04:45)
Revealing mistake: When Pacey and Rich are physically fighting in the office, there is a quick shot of a person who is supposed to be Pacey leaning forward over Rich and hitting him. However, if you look closely you can see that the hair on this person although dark brown, appears much longer and curlier than Pacey's current hairstyle. Also-just before that shot ends, you can see the longer hair swing away from his neck loosely on the right side. The next shot of Pacey shows his shorter haircut, so I believe the longer hair was actually a stunt man substituting for Pacey in a risky, physical scene. (00:40:00)
Audio problem: Just after Audrey storms out of Pacey's apartment, after catching him with Alex; Pacey runs after her and they begin arguing in the street. Audrey makes a comment that 'it meant your arms around her, and HER tongue down YOUR throat' referring to the kiss between Pacey and Alex. But then Pacey counters with 'well actually, it was HER tongue down MY throat' in sort of a comic way, as if he was correcting a backwards situation. But Audrey had just said the same thing! One of the Actors messed up their lines, probably Busy Phillips since Joshua Jackson seemed to have his lines correctly.
Continuity mistake: During this scene towards the end, Bessie insists on putting lipstick on Joey for Graduation. She dabs it on quickly, and there appears to be a noticeable smudge or mark on Joey's upper right lip from the lipstick. But the next shot of Joey, the lipstick suddenly appears normal and perfectly applied, and the smudge is gone. (00:33:40)
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)
Continuity mistake: When Aunt Gwen is talking to Dawson and Joey in the store, just after she says, "General all around cuddliness between the two of you"; Joey is facing her and Dawson is turned the other way, with his back to her. But the next shot of Dawson is a close-up, and he is suddenly facing Aunt Gwen as he says, "OK, I'll tell you the long soap opera short". The transition was too fast to be realistic, or to have given Dawson enough time to turn completely around to face Aunt Gwen.
Revealing mistake: When Dawson arrives home after his evening with Gretchen and friends, his Mother is seated on the couch waiting up for him. As she talks to him, she stretches back, still seated on the couch; and you can see on her stomach the outlines of the padding she is wearing to make her appear pregnant when she really isn't. (00:35:25)
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.
Audio problem: During the Season Finale Narrative, second half- Creator Kevin Williamson mentions that the kiss between Doug and Jack on the beach was "the second gay kiss in the show". He's a bit mistaken, as this was actually the 4th gay kiss in the entire series. Jack kissed Ethan in Season 3, Toby in Season 4, David in Season 6, and Doug in the Season Finale. (01:36:00)
Revealing mistake: In the very beginning of the episode, Pacey is watching TV and gets up to look out the window towards Hell's Kitchen. As he moves back from the window, he accidently bumps the kitchen counter/cabinets. An entire section of 'counter/cabinet' moves noticeably; revealing it to be a cheap, flimsily-built fake kitchen counter/cabinet instead of a more substantial, real one. This was obviously just part of a set.
Continuity mistake: At the beginning, Pacey and Joey are dining at a large table while Pacey is flirting with the woman on his right. Joey goes underneath the table to retrieve her shoe, and sees what is apparently the woman's left hand on Pacey's knee. But the very next shot of the woman above the table shows her right hand up against her face, and her left arm folded, hand on the table. Her left arm doesn't appear to have moved, and there was no time for a transition from Pacey's knee to above the table. (00:00:55)