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: At the end of the episode, Dawson is seated in the kitchen talking to Pacey in a normally loud voice. At the same time, Joey and Charlie are awake and talking in the pup tent in the living room, very close to the kitchen. Later in the Season we learn that Joey had no idea Dawson had driven down to Florida to see her, as apparently he left without seeing or talking to her. But being in such close proximity that morning; there is no way Joey would not have been able to hear Dawson's voice as he talked with Pacey. The living room was close enough to the kitchen, so it doesn't make sense that Joey wouldn't have known Dawson was there and if she did-she would have gone to talk to him.
Plot hole: Jack and Joey are desperate to get the tank pump fixed so they can put the lobsters back in. However, once the customer tells them how to fix it, they then stop for a chat, check his table for tips, read a poem, share a moment, and start cleaning counters - with no attempt to re-house the lobsters.
Revealing mistake: During the scene when Dawson and Gretchen are talking on the bridge, two couples walk by in the background. An older couple passes from left to right, and a younger couple walks from right to left. The younger couple is a woman with blonde, curly hair wearing a green top and beige/white skirt, and a guy wearing a green or blue top and white pants. During the same scene, the same younger couple again walks by in the background from right to left two more times. Then the older couple walks by again from left to right. Then one final time, the younger couple walks by yet again for a fourth time from right to left. Guess they were using the extras a lot that day.
Factual error: When Jack and Andie are talking at the dinner table about her cheating on the PSAT, Jack says, "Do you really want to get kicked out of school for cheating on something that has the world 'Practice' in front of it?" PSAT actually stands for Preliminary Scholastic Aptitude Test, not Practice SAT. This is the same mistake that Pacey made in an earlier episode.
Plot hole: When everyone is staying at the Potter B&B, Joey mentions that it's supposed to be the coldest night of the year. Also, Mr. Fricke tells them at breakfast that the heat went out again during the night. After such a cold night and the heat going out, the house must have been freezing that morning. Yet Joey wakes up and is wearing only a skimpy sleeveless top and PJ bottoms, more like summer pajamas. She continues walking into the very cold house without putting a robe or anything else on. It looks a bit odd, considering how cold the temperature is and the fact that everyone else that morning is already wearing long sleeves. Later that morning, the house is still so cold Joey is sleeping by the fire with a blanket over her. Yet earlier that morning, she seemed to be comfortable in scanty summer PJs.
Continuity mistake: When Joey is talking to the Mugger in the hospital room, every time they show her sitting down in her chair or getting up from it the chair looks like it is quite far from the bed, down past the foot of the bed, about 10 feet or so from the guy. But all the other shots she appears to be sitting much closer, only a few feet away from his face.
Factual error: In the third scene, when Doug stops Jack for speeding, both vehicles in the scene have North Carolina state safety inspection stickers in the lower driver side windshields, as opposed to a Massachusetts inspection sticker (which would be on the passenger side).
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).
Factual error: During the Pilot of Dawson's Creek, Joey mentions to Dawson that they are about to "Start High School" soon, implying they are just entering High School for the first time. When Jen shows up in the taxi for the first time, they also tell her they are Sophomores as well as she. I assumed this must be a High School that begins with Sophomore grade, meaning Middle School in their area must have been 6th or 7th through 9th grade. The entire first two Seasons of the show are their Sophomore Year. But in Season 3, during their Junior Year Jen meets Henry, a "Freshman". He is repeatedly referred to in the show as a Freshman, although technically Capeside High is supposed to be 10th through 12th grade. This makes no sense timewise, as there are no Freshmen at that school. The main characters all started High School as Sophomores. Also-there is a trivia section on one of the DVDs that lists certain classes/teachers the main characters had as Freshman English, etc. But since they had those classes/teachers in the show, they were really Sophomores which further verifies there are no Freshmen at the school.
Audio problem: At the end of the episode when Pacey and Joey are paying for their items, Pacey launches into a philosophical speech. The cashier has asked him whether 'they found everything they were looking for' and he answers no, but they found what they needed, which was even more important. He then elaborates, explaining that 'if you found everything you needed that day, what would be the point of doing it all over again the next day'. But Joshua Jackson apparently messed up his dialogue, because the point he was making was that they didn't find everything they were looking for, not what they needed. He was making the point that they did find everything they needed, so it would be contradictory to then explain that there was no point in finding everything you need. He meant to say 'if you found everything you wanted (versus needed), what would be the point of doing it all over again the next day'. Oops.
Plot hole: After Drue has spent the night at Jen's house, Grams explains to Jen that she had a nice talk with Drue right after Jen left for school. But this doesn't make sense, because why would Jen have to be at school a certain time, and Drue not go to school at the same time or at all? His attendance at school would have been required as well.
Revealing mistake: When Joey and Pacey are talking in the car as Pacey drives them to the Train Station, you can see at least 3 lanes full of cars and a great deal of traffic behind them. But when Pacey suddenly turns right, off the main road and into the entrance to the Train Station; you can see that suddenly the main road he has just turned off of is almost completely empty of any traffic in either direction, except a truck that drives by at the last minute. It also appears to be a smaller road. Apparently the scenes with their dialogue in the car were shot with background video that wasn't the actual location.
Continuity mistake: When Joey is talking to Eddie in her dorm room, she is facing him with her hands resting firmly on his shoulders. In one close-up of Joey, her hair is hanging in front of her right ear. In the next shot of her, the hair on her right side is suddenly tucked behind her ear. Her hands haven't moved, and no-one touched her hair.
Plot hole: When Dawson runs into Grams at the Airport, she asks him to not mention her trip to Jen. But shortly after that in the same conversation, Dawson invites Grams to go say hello to Jen and Jack who are waiting for their flight. If Grams didn't want Jen to know about her trip, she couldn't very well just go meet Jen without explaining what she was up to.