Continuity mistake: In "The Te of Pacey", Pacey's birthday takes place in winter - it is snowing and everyone is wearing heavy clothes. The other episode featuring his birthday, season 2's "Crossroads", takes place in summer (everyone is wearing shorts and light shirts).
Continuity mistake: During this episode, Jack injures his left shoulder playing football and has to wear a sling the entire time. Every single time Jack is shown, he is wearing a blue sling on his left arm, with the supporting strap across his right shoulder (to provide diagonal support), except once. During the party scene when Jack is talking to Dawson - the blue sling is suddenly over his right arm, with the supporting strap across his left shoulder. This scene was actually shot with the sling on the correct arm, but was "flipped" to make it fit with the direction of the next scene to follow. (00:29:45 - 00:33:40)
Plot hole: When Pacey and Andie are talking at the Senior Party, she excitedly mentions that he will be in the Caribbean that Summer. Pacey says that Andie would be in Florence, Italy. This doesn't make sense, because at that point in the episode, none of Andie's friends knew she was returning to stay in Italy. In fact, later during the graduation ceremony, Andie is talking to her brother Jack. He is the first person she tells the news to, and even says, "I haven't told anyone else this". So how would Pacey know the night before that Andie had decided to stay in Italy longer? (00:30:45 - 00:37:25)
Plot hole: When the storm hits the Capeside Yacht Club, Andie takes charge and tells Mrs. Valentine to write down two phone numbers and call Dawson's parents, and Jen's grandmother. But she forgets completely about Joey and Pacey, both of whom are in harm's way, especially Pacey. Seems illogical she would have Mrs. Valentine call about two of the people out at sea, but not the other two. Joey's family and Pacey's family would also be concerned.
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.
Plot hole: While out at sea, Jen and Pacey get slammed by the storm. So Pacey decides to take shelter at a small cove that he and Dawson had once used to wait out a storm. Pacey and Jen make it safely to the cove, and wait on the boat in fear of being capsized or drowning. If they are in a cove, and close to shore-why wouldn't they go on land to wait out the storm where they would be safer than in a boat that could be capsized or flooded? They could have probably swam a few feet to get to the shore, since they were already in a small cove that was near land. When Pacey was steering the boat into the cove; there was a noticable man-made jetty they were very close to, so obviously they were within close range of solid land.
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)
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.