100 Light Years From Home - S5-E19
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: 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. (00:20:40)
High Anxiety - S5-E6
Plot hole: In the beginning of the episode, Dawson is talking to his Doctor about seeing a Psychiatrist for his panic attacks. The Doctor mentions the name of one in Boston, and calls out to the assistant to make an appointment for Dawson. But only about 12 seconds (real time) later, the assistant suddenly comes in and already has made an appointment for Dawson the next day at 5PM. There is no way the assistant could have possibly gotten ahold of a busy Psychiatrist in Boston, and made a confirmed appointment for Dawson in only 12 seconds. It would take longer than that, especially as most Psychiatrists have phone menus where they have to return calls from. (00:01:25)
100 Light Years From Home - S5-E19
Plot hole: When Chris arrives at the beach house, and invites everyone to the MTV concert a few blocks away; he tells them to follow him there implying that he can get them in free with his 'clout' as a movie star. But later during the first song, Joey and Charlie arrive walking up the stairs from the beach apparently just coming from the beach house. They walk right in to the concert area - no problem. But how would they get in without Chris? They didn't have tickets, and Chris wasn't with them to usher them in. It wasn't likely an event open to the entire general public; as it would be too crowded, and not just the younger people MTV audience for TV.
Plot hole: Dawson and Audrey are planning to fly to LA together, and he already mentioned to Audrey that he needs to stay at her family home for awhile. But then at the end of the episode; Pacey talks Audrey into driving to LA with him, and Dawson is left to fly to LA by himself. Wouldn't this make for a very awkward situation if Dawson flew to LA a few days before Audrey arrived by car, and had to stay with her parents completely by himself having never met them before? Doesn't seem like something Dawson would do.
Plot hole: When everyone first shows up at the Airport, it's daytime and not too late. Joey then works an entire shift at the Capeside Yacht Club, probably through the dinner rush until later that night. When Joey and Pacey are talking on the dock after she is through working, it's late at night. They suddenly decide to rush to the Airport where they assume everyone is still waiting for their flights. Being as this must be several hours later since they all met at the Airport, would everyone's flights really be delayed that long? (00:30:05)
Downtown Crossing (2) - S5-E15
Plot hole: When Joey suddenly regains consciousness in the ER, she is sitting upright on the end of a hospital bed or gurney. But this doesn't make logical sense, because if she were really unconscious she would be laying down. Yet it's made very clear in that shot, that she is opening her eyes for the first time after fainting and being unconscious.
Answer: It's only explained once in the series. Jack says to Andie "I tried to start kindergarten without you", meaning Andie was smart enough to start school early.