Revealing mistake: When Doug stops Pacey on the street to talk to him, Pacey turns to face Doug (and the camera). You can see at this point, the microphone sticking out from Pacey's upper shirt. (00:04:25)
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)
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)
Deliberate mistake: During this scene when Dawson and Joey are getting ready to graduate, the actor James Van Der Beek asked to ad lib his dialogue. He did, and what ended up on the air was his improvised version of the lines that had been written in the script. (00:39:30)
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.
Continuity mistake: Right before the graduation service, Dawson is joking with Joey to get her mind off her speech. The wind has blown Joey's tassle so it's caught partly on her left ear facing the camera. But in the next shot of her, the tassle is suddenly hanging normally in front of her ear. She hadn't appeared to move her hands.
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.