Factual error: In the third scene, when Doug stops Jack for speeding, both vehicles in the scene have North Carolina state safety inspection stickers in the lower driver side windshields, as opposed to a Massachusetts inspection sticker (which would be on the passenger side).
Revealing mistake: During the scene when Jen is telling Jack about her illness in the hospital room, she asks him to get into bed with her and talk. As he does that, Jen lifts her right arm to allow room for him. There is a tube attached to her right arm at the inside of her elbow, that is supposed to be going into an artery. But you can see that the end of the tube is actually pointing the opposite way, and sticking up through the tape pointing towards us. Obviously this was because they couldn't actually insert the tube into Michelle's arm for the scene.
Factual error: When Jack is carrying Jen out of Pacey's restaurant, she bends her head down. You can see that her now very long, curly hair is real and has a natural part. But this episode was in reality filmed right after the preceding episodes in Season 6, not 5 years later. And in the later episodes of Season 6 Jen had dramatically shorter hair. Although in the context of being 5 years later Jen's much longer hair makes factual sense, in reality it isn't possible that she could have grown her hair out that quickly between the Finale and the episodes filmed before it. So how did she? The shorter hair didn't appear to be a wig.
Continuity mistake: When Joey and Pacey are standing in his restaurant, watching Dawson and the others come there is a shot of Joey with her hair tucked behind her right ear. But in the next shot of her, a close-up, she suddenly has all her hair pulled forward around her face. Her arms haven't moved between shots.
Plot hole: When Jen and Jack are talking at the B&B, he picks up the bottle of pills from Jen's purse and asks her about them. She lies, telling him they are pills for Grams when in reality they are Jen's medication. But Jack is examining the label closely, and wouldn't he see pretty easily that Jen's name was listed instead of Grams? He had plenty of time to read the entire label.
Continuity mistake: When Jack is pulled over near the start the creek behind him is empty, and remains like that throughout the scene. Then for the last few shots before he drives off again a sailboat has appeared in the background, literally out of nowhere.
Plot hole: Dawson is in his bedroom, and hears a noise outside his window. He panics, and picks up his laptop to use as a 'weapon' if necessary, while approaching the window. This doesn't seem logical; because for one thing he knows Joey is in town and she has been coming in through that window for years, and wouldn't he think of that first? Also-highly unlikely Dawson would actually use a very expensive Apple laptop as a weapon when it could be damaged, and he relies on it extensively for his work as a Writer/Producer.