Plot hole: During the Leery's Christmas party, Jen asks Jack which colleges he applied to in her name. He replies: Bard, Brown, Columbia, Emerson, Sarah Lawrence, and BU (Boston University). But later in this season, Jen goes to visit NYC because she was accepted into the University of New York. How could she have been accepted there when she never applied? Jack didn't apply for her there, and she didn't fill out any college applications herself.
Continuity mistake: When Jen and Jack are talking in her room, Jack asks "Have you finished your applications yet?" Jen is rubbing her hands together in front of her. But the next shot, suddenly Jen's arms are stretched back behind her. Too sudden to be a realistic transition.
Continuity mistake: When Jen and Grams are arguing in the kitchen, Jen says "Why don't you donate to someone who cares". At this point, Jen turns to face away from Grams. But the next shot shows Jen suddenly turned towards Grams, facing her. Later in the scene when Grams says "Why don't you take the time to fill out a couple of your college applications", Jen is turned towards Grams. But the next shot suddenly Jen is facing away from Grams again. Apparently this scene were filmed two separate times, and edited together.
Continuity mistake: When Joey comes out of the changing rooms, her left dress strap is slipping off her shoulder in the shots from behind, but sits correctly on her shoulder when viewed from in front.
Continuity mistake: When Dawson is helping Gretchen to hang mistletoe, his arms change position instantly between shots, from laid on the ladder, to above his head touching the mistletoe.
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.