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.
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)
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)
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.
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)
Revealing mistake: This scene of Dawson and Joey in the parking lot of the "Dive-In" was not really filmed in the same location. The show only had the location of the "Dive-In" for a limited time, and had to film all other related scenes in the parking lot of the studio in Wilmington, NC. Any scenes that don't show water in the background; and are just palm trees, lighting etc. were actually shot several weeks later in the parking lot, which was recreated to be part of the beach at the "Dive-In". (00:33:30)
Revealing mistake: In the first scene, Pacey says something like see I think we should probably drop anchor here, have a bite to eat (and other things)... As he's walking around the boat, the camera shifts over and you can see two ropes that indicate the boat is already anchored or docked to something.