Pilot (aka Emotions in Motion) - S1-E1
Deliberate mistake: Throughout the first episode, Jen's bangs are long in scenes relating to her "Grams" and short in all other scenes. This is because the scenes involving her storyline with Grams was shot much later, after the show was picked up. (00:05:45 - 00:16:15)
Coming Home - S4-E1
Deliberate mistake: This scene between Dawson and Jen in his 'dark room' was shot in a distinctive red light. However, in reality there was no red light during filming, the effect was added later during post-production. (00:19:25)
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)
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.