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.
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.