Coming Home - S4-E1
Plot hole: This scene reveals that Joey has brought Dawson a special gift from her sailing trip with Pacey. It's a brick from the foundation of Ernest Hemingway's home in the Florida Keys, symbolic to 'build the foundation of a friendship' between her and Dawson. In reality, it's highly unlikely that anyone would have allowed Joey to damage a foundation wall by prying out a large-sized brick; and steal it from the premises of a famous, historic home and landmark. (00:36:15)
Coming Home - S4-E1
Plot hole: Dawson mentions to everyone on the beach, that he and Jack have to go paint their 'last home of the season', implying they have been earning money by painting homes around Capeside. However, when Dawson and Jack stop by the hardware store to get supplies, Dawson picks out a metal handle for the paint rollers. Paint and new rollers makes sense, but if they have indeed painted other houses that Summer, he probably wouldn't need a more substantial piece of equipment as the heavy duty metal paint roller handle. He would already have one.
Coming Home - S4-E1
Plot hole: Dawson and Jen are in a small 'darkroom', developing photos and speaking at a normal level. This darkroom is located just behind the main stairs, and very close to the living room where Dawson's parents are 'getting busy'. Therefore, the parents normally would have heard their voices so close to them, and known they were in the house and not been so surprised by them.
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.