Factual error: When Jack is carrying Jen out of Pacey's restaurant, she bends her head down. You can see that her now very long, curly hair is real and has a natural part. But this episode was in reality filmed right after the preceding episodes in Season 6, not 5 years later. And in the later episodes of Season 6 Jen had dramatically shorter hair. Although in the context of being 5 years later Jen's much longer hair makes factual sense, in reality it isn't possible that she could have grown her hair out that quickly between the Finale and the episodes filmed before it. So how did she? The shorter hair didn't appear to be a wig. (00:26:20)
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 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?
Other mistake: After Dawson and Jen order "cokes" from Joey at the seaside restaurant, Joey pours their drinks into plastic red cups. She only pours several milliliters of cola into the cups, barely enough for one gulp. (00:29:50)