Continuity mistake: When Jen walks into the Video Store, she is wearing a black top, red skirt and a black leather jacket that is completely open and unbuttoned. As she talks to Dawson, who is behind the counter, she says, "I'm working on a project with Pacey in a 'human growth and development' thing - is he here?" She is standing up, but leaning slightly forward against the counter and her coat is still widely open. But the next shot of Jen, as she says, "But he told me that he was working today," the black leather jacket is suddenly closed together as if buttoned, and she is leaning foward more on the counter. Then, after Dawson walks over to the movie rack and Jen follows him, her jacket is again hanging completely open and unbuttoned.
Continuity mistake: When Jack and Andie are using the computer with Ben's Instant Message on the screen, there is a close-up of the computer screen as they wait for Ben's photo to download. Just to the right of the photo is the entire IM, which shows all 3 lines of dialogue between Ben and Jack. The last line says, "So. What do you think?" But after the photo is finished, there is a sudden 'beep' from the computer signalling another incoming IM message, which Jack then reads out loud as if it is a new message. But what he reads is, "So. What do you think?", the exact same line that was already in the IM box before the photo finished downloading. The implication is that he is reading a message that just came in, yet that line of dialogue from Ben was already present in the IM box previously.
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 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.