Coming Home - S4-E1
Continuity mistake: When Joey and Pacey are on the boat Coming Home, look closely at Pacey's hair under the cap he is wearing. It is longer/thicker hair, and appears to be layered somewhat on the sides and back of the neck. A little later when Joey and Pacey have docked in Capeside and are getting off the boat, Pacey's hair is suddenly cut very short/close to the head, and does not look like it did under the cap on the boat. (00:00:50 - 00:05:05)
Coming Home - S4-E1
Continuity mistake: Gram's kitchen in previous Seasons had orange walls, and the cabinets were painted with avocado green and orange centers. (Except for the Pilot Presentation, where the cabinets were painted all green). However, in this scene the walls are still orange but the cabinets have been suddenly changed to avocado green and yellow centers. (00:15:35)
Coming Home - S4-E1
Continuity mistake: When Joey and Pacey are talking on the dock just after arriving back in Capeside, Pacey has a bag over his left shoulder. In shots from in front the bag's strap is folded over itself, but in shots from behind it lies flat on his shoulder.
Coming Home - S4-E1
Continuity mistake: Just before Jen gets up from the sun lounger, the cord from her sun hat goes instantly from falling off her shoulder to sitting by her neck.
Coming Home - S4-E1
Continuity mistake: When Joey and Pacey are talking on the dock just after arriving back in Capeside, Joey's hair changes instantly from being swept behind her right shoulder and behind her back, to sitting in front of both shoulders.
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.