Continuity mistake: At the end of the episode, when Pacey is telling Joey about his school problems; her hair changes dramatically between shots. Just as she says, "Whatever it takes, we're gonna fix it", her hair is blown back off her right shoulder, away from her face with only the hair ends resting on her shoulder. The next shot of Joey, as she says, "I'm not going anywhere without you", her hair is suddenly down in front of her right shoulder, and close to her face again. When Pacey asks her, "Joey?" and she replies, "Yeah?", her hair is still fully down by her face on the right side, in front of her right shoulder. But then the next shot of Joey when she says, "I'm not that much smarter, Pace", her hair is suddenly swept far back off her right shoulder, away from her face with the hair ends resting on her shoulder again. It looks like they filmed this scene two different ways, and edited it together.
Plot hole: When Dawson goes over to Joey's house to talk to her about Pacey's school problems, he mentions that Pacey had missed that entire day of school. Joey apparently didn't know this, as she is surprised at the news. Since Joey and Pacey are closely involved - wouldn't she have noticed his absence at school that day already? Surely she would have noticed Pacey missing for an entire day of school.
Plot hole: Mrs. Valentine almost fires Joey, after discovering that she lied about knowing the Owens. Drue steps in and saves Joey's job by claiming he did see the Owen boy. But Joey keeps her job throughout the rest of that season. Since the Owens were said to be in Paris only until the 1st of the year - wouldn't Mrs. Valentine have found that Joey lied about knowing them as soon as they returned to Capeside? Surely Mrs. Valentine would have mentioned Joey to the Owens; thinking she was their good friend, and because she was new on staff at the Country Club they were members of the board for. And once she found out Joey had indeed lied, why did she not fire her at that point?