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.
Suggested correction: Eve closed the window before they hid under the table.
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.
Suggested correction: You have it backwards. To be a 16-year old freshman Henry wouldn't have skipped a year - he would have had to repeat one. As you put it, he's not exactly "intellectually motivated," so it's plausible to think he did indeed repeat a year.
A Weekend in the Country - S3-E12
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?
Suggested correction: Bodie didn't make the pancakes (at least not all of them) it was his recipe.