Continuity mistake: When Joey and Pacey are arguing in his office, there is a close-up of Joey with noticable hair strands hanging off both sides of her face. The next shot of her, the hair strand on the left side of her face is suddenly gone, and her hair is tucked behind the ear on that side. This entire time Joey has been leaning forward on Pacey's desk, her arms supporting her. The next shot of her, the hair strand on the right side of her face is gone. But the next shot, both hair strands are magically back. (00:32:20)
Continuity mistake: When Pacey and Joey suddenly start kissing in Pacey's office, Joey's hair is still tied up on top of her head. They turn and fall on the couch, and Joey's hair is suddenly completely loose and long beneath her. At no point during this transition did anyone touch or undo her hair. (00:33:10)
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.