Visible crew/equipment: When Joey is in Dawson's room, trying to tell him about her relationship with Pacey, she can't find the words and turns to leave. As she bends over to climb back out of his bedroom window, you can suddenly see a microphone wire protruding from the back of her white shirt. It's a visible vertical line, and as she continues to climb out the window, you can see that there is no mike pack on her lower back.
Factual error: In the second segment of this episode, there is a scene where Joey bumps into Dawson on a street corner after she has just left the library. As they are talking, there suddenly appears in front of them a large square stone monument which describes the 'North Carolina' battleship. The 'North Carolina' is a large battleship that is permanently stationed at the pier in Wilmington, NC where the show is really filmed. They had to shoot around this large ship constantly, being careful not to let it show as they are supposed to be in Capeside, MA. However in this scene, they accidentally filmed right in front of the large square monument which shows several lines of writing. On screen you can read: "On the west side of the river a little south of the causeway was Beery's Shipyard, where the Confederate ironclad North Carolina." This is apparently in reference to the battle ship 'North Carolina' which is stationed nearby in their location of Wilmington, NC not MA. Oops.
Continuity mistake: This episode shows a full day's events repeatedly in 4 separate segments, and it appears they reused the same scenes and dialogues. But there are noticable differences between Act 3 and Act 4. At the end of Act 3, when Dawson confronts Joey and Pacey about their relationship; he says to William and Andie, "Better yet, ask Joey. Ask her how long [she's] been lying to me and to you." During this same scene in Act 4, Dawsons varies it slightly: "Better yet, Ask Joey. Ask her how long [the two of them] have been lying to you and to me." He also switches 'you and me' interchangeably. Act 3, Dawson further says, "Go ahead ask them, because I can't [stand to look at them]." But in Act 4, he changes it to "Go ahead ask them, because I can't [even stand to look at them anymore]." The way these two scenes were shot varies also. During Act 3, when Dawson is finished talking he storms back into his house, and makes it inside the inner front door alone. But in Act 4, Dawson starts running back into his house with Joey following close behind him, so that she is in the frame when he reaches the inner front door.
Plot hole: At the beginning of the episode, when Joey and Pacey are kissing in the boathouse on the dock; he lifts her up and puts her on a counter right in front of a window. This window appears to look directly out over the nearby boats and dock, meaning they would have been in full view of all their friends waiting to christen Pacey's boat. Not very logical to be kissing on the sly, right in front of a window where everyone could see them.