Corrected entry: When Jack and Jen are talking at the beginning, Jack tells Jen that "She hasn't had sex the entire time he has known her". But this isn't true. Jen did have sex with Chris, the 'cool guy' who invited everyone over to his house to study for the big exam in Season 2. And Jen had known Jack by this time; as she met him previously during the school dance where Jack confronted Joey about their kiss.
Corrected entry: When Joey and Pacey are talking while walking on the beach, Pacey makes a point of telling Joey that Dawson is her past, present and future. But later, when Dawson arrives and asks to see Joey-Pacey suddenly becomes very negative and tells Dawson that he should give up on any relationship with Joey because "it's over". This doesn't make sense for Pacey to contradict himself so strongly, and it was rude and hurtful for him to tell Dawson that. Especially when earlier in the Season during the funeral episode, Pacey told Joey that 'he was all for those two (her and Dawson) having their shot'.
Corrected entry: When the Mugger asks to see Joey, the Dr. explains to Joey about his condition as they walk to his hospital room. The Dr. tells her that the Mugger had undergone surgery to try to save his life, and had a 'sucking chest wound' which is obviously a substantial injury. Yet when they show the Mugger in the hospital bed, he is bare from the waist up. There are absolutely no signs of surgery or incisions anywhere that can be seen on camera, which is illogical considering all his internal bleeding and a massive chest wound.
Corrected entry: During Jen's 'Scary Story' at the radio station, they show her playing an old fashioned vinyl record as her last song for the night. This is especially apparent when it starts skipping, and she finally runs back in to remove the needle from the vinyl. But this is the 21st century, and it would be likely that a trendy, major college radio station would not still be using vinyl records. They would be more likely be using newer technology and CDs.
Corrected entry: Early in Season 5, Dawson flies from LA to Boston to visit Joey for the weekend. He only brings a weekend-type bag for the trip, since he's planning on returning to LA after the weekend. But-Dawson doesn't go back to LA until the very end of Season 5. Because of Joey's phone message, he decides to stay in Boston and eventually decides he isn't going back to USC at all. Meanwhile, we never see Dawson fly back to LA to collect any of his belongings from his dorm room at USC. He left most of his stuff there, when he flew out to see Joey for the weekend. But during the rest of the Season, he never goes back to retrieve all of his things from LA, and never has anything shipped out to him or put in storage. So what happened to the rest of Dawson's stuff back in LA? Particularly in his USC dorm room? He probably retained his dorm room for the rest of that semester, since it was only October when he went to Boston. Yet he never goes back to get his 'stuff'. This doesn't make sense, as even though he wasn't sure about USC at first he makes a final decision in episode 7. Dawson doesn't go back to LA until the end of the school year, for the Summer-and his dorm room was probably assigned to someone else for the second semester at USC. So how did he ever get the rest of his stuff from LA? This is never explained at all during the show.