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.
Plot hole: Jack and Jen go to Capefest, primarily because Jack wants to run into Ethan who invited him there for the festivities. Jack and Ethan spend time together at Capefest, and become friends. Ethan makes a comment that he wants to go straight to sleep because he is tired, and the next day was a big day, meaning 20 bands starting at dawn. But the next morning, before breakfast Ethan and Jack talk briefly, Ethan says 'Goodbye' and they go their separate ways without enjoying any of the music fun together. It doesn't seem plausible that Ethan would invite Jack to Capefest to enjoy the music scene, and then take off just when all the fun is starting on the main day. Why wouldn't they have spent the day together as friends enjoying all the bands and festivities which is what they went there for?
Plot hole: When Jen is helping Dawson at the Video Store, and spots Pacey and Joey out on the street, she asks, "Dawson, do you have one of those little signs that says 'Back in 5'?" Dawson then relies "Yeah", implying he could leave the store for several minutes on a small break. But then he and Jen follow to where Joey and Pacey are taking their dance lesson. Dawson then proceeds to dance his way through an entire dance lesson, witness a confrontational scene in the coat closet, and then lingers outside in the street having a meaningful conversation with Joey. This would all obviously take up a considerable amount of time, much more than a small break. Therefore - how would he have gotten away with closing down the Video Store for that amount of time without losing business and possibly his job? Especially if the sign only indicated he would be away a few minutes. This would be very un-Dawson-like to be that irresponsible with his only place of employment.
Plot hole: When Dawson and Eve are in the PSAT room After Hours looking for the test, there is a noticeably open outside window behind them implying that was how they broke into the room. But when the security guard suddenly comes in the room and walks by the window twice, he makes no attempt to close the window and secure the room, which one would think was his job.
Plot hole: When Jack and Andie are using the computer at school, Jack shows a clear knowledge of computers by explaining search engine criteria to Andie. It's also mentioned that they had already done an extensive background check on Ben, again implying that Jack has extensive computer skills. So why would Jack, who is apparently quite skilled with computers: not know what an Instant Message is, not know how to 'get rid of this thing' by clicking off the IM window, and not know to click 'Send' in order to send an IM back to Ben. It doesn't make sense that Jack would know so much about computers, and not have any awareness of how something as simple and basic in Internet usage as 'Instant Messages' would work.
Plot hole: When Dawson picks up the phone in his bedroom after seeing the lights in the house next door, he dials 9-1-1 (You can hear the three beeps from the phone buttons). Yet when the person on the other end answers the phone, she says "Capeside Police". Later in the episode Doug also makes a reference to Dawson dialing 911. Yet when he called 911, they should have responded "911" instead of "Capeside Police". Normally when you call 911 you would get a 911 operator, not be put directly through to the local Police until you requested it.
Plot hole: When Jen and Henry are talking in the park, he tells her that he's 15. But later in Season 3, he has a Birthday party at the Skating Rink in which he would have to be turning 16. Henry is a Freshman, and it's highly unlikely he would be turning 16 in his Freshman year. All the main characters of Dawson's Creek turned 16 during their Sophomore years. It also doesn't seem likely that Henry would have skipped an academic school year, as his personality/character doesn't appear to be intellectually motivated.
Plot hole: The morning after everyone stayed at the Potter B&B, there is a fun kitchen scene showing all the kids dancing together preparing breakfast. Andie seems to be making pancakes. Yet later at breakfast, Joey finds out that Bodie has come back and is the reason the pancakes taste so good. Apparently he was the chef that morning, but he is nowhere in sight during the breakfast-making scene. So if all the kids are cooking - where is Bodie? Wasn't he supposed to make the pancakes?
Plot hole: When Dawson and Eve are in the PSAT room After Hours, looking for the test, a security guard suddenly comes in. They both have time to duck under a desk and avoid being seen, but as soon as the guard passes them, they start talking in rather loud whispers. The guard is still very close to them, as he quickly returns to walk past them going the other way. It seems reckless for them to be talking like that with the security guard so close at hand who would normally hear them, and so soon after he walks by them.
Plot hole: When Dawson suddenly shows up at Joey's workplace, Joey is inside asleep at the desk and Pacey is awake sitting outside. As Pacey and Dawson start fighting verbally, their voices escalate loudly but Joey still doesn't wake up even though she's sitting right inside. It isn't until they start throwing punches at each other and fighting physically that Joey suddenly comes running out to see what is going on. It doesn't seem realistic that Joey would be able to sleep through their loud arguing, and not wake up until they are hitting each other. If she had woken up before that, she would have definitely come outside to see what Dawson and Pacey were up to.
Plot hole: Joey tells AJ that her Mother used to read "Little Women" to her, and in fact named her 'Josephine' because "Little Women" was her favorite book. But in a previous episode when Joey and Dawson visit her Mother's grave, the gravestone has printed 'Lillian Josephine Potter', meaning her Mother already had Josephine as her middle name. So naming Joey 'Josephine' wasn't only because of the book "Little Women"; her Mother more likely named her that because it was her middle name.
Plot hole: During this ending scene, Joey runs frantically to find Pacey and asks to go with him on his sailing trip all Summer. She is carrying absolutely nothing with her, not even a purse or wallet. Her pockets are completely flat, and she doesn't even appear to have ID. Joey's lack of luggage or clothing is explained in her dialogue, as she jokes about the next change of clothing. She probably assumed she could buy what she needed along the way, and was in a hurry not to miss Pacey's departure. But it doesn't seem logical that she would take off for an entire Summer without any type of purse, wallet, money, credit cards, ID, etc. as she would have no way to pay for anything. She would also need her ID in order to work the odd jobs she mentions in Season 4. (00:39:10)
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.
Plot hole: When Dawson, Joey, Jen and Pacey are stuck on Witch Island after dark-they are suddenly shown using strong flashlights to see their way. But they had never originally intended to be on Witch Island after dark, which was made clear when someone suggested leaving because 'it was starting to get dark'. They were only carrying light daypacks for their day trip, and Pacey even joked about how no-one had bothered packing any snacks. Therefore since no-one intended to be on the Island after dark, and they packed very light day packs without even food, why would they suddenly be carrying large flashlights? It's unlikely they would have bought them at the Witch Island Gift Store, as it wasn't shown and no-one seemed to pay for anything from there.