When Shaggy and Scooby crash on Ben, Velma and Fred after escaping the Witch's Ghost, Daphne is nowhere to be seen. But after some explanation, Daphne is then heard and appears under Fred.
The timing of Ben finding the gang's Moat Monster case is inconsistent with how it was depicted in Scooby-Doo on Zombie Island (1998). In the previous film it was a case long ago for the gang, but Ben is just finding it as if it's recent. The photo also troubles the timeline, as Daphne and Fred both wear the new outfits introduced in the previous film, when they should be wearing their original ones, making it appear as if that case had been retconned as one of the newest ones.
While a visual reference is made to a the case shown at the start of Scooby-Doo on Zombie Island (1998), this film otherwise ignores everything accomplished in that film, including Daphne's status as a famous journalist, and their discovery that monsters really exist. Now they are back to being wandering teens, and unprepared for a supernatural threat.
When Shaggy tells Jack that he and Scooby will have two orders of everything, the booth next to them is noticeably empty.
The gray hair around the male African American tourist's head changes with each turn he makes as he talks.
While the Wiccan religion did not appear until the 20th Century, it has a built-in secret-history mythology. It is common for films involving Wicca or similar religions, to treat this mythology as the in-universe truth. The idea that Wicca is passed down by blood is a bit unconventional, but the power of lineage is a common plot device in fantasy, so for 70 minutes it can be treated as true.
There seems to be possible confusion over the gender of the female African American tourist's partner. From afar the partner looks to be a male with a ponytail, but close-up shots have the partner looking more feminine wearing lipstick and has breasts. While non-binary or intersex people were not well-known in the 1990s, they indeed existed then.
None of the people watching the Hex Girls perform "Earth, Wind, Fire, and Air" are the tourists from the beginning of the film. It's possible the ones who are watching it are locals.
Thorn looks like she's waving to the viewer(s) as opposed to the audience watching them. The Scoobyverse has a long tradition of randomly inserting cute moments that break the fourth wall.
In the last shot of some of the tourists watching Shaggy in the pillory, the blonde mother disappears. Possibly because she's already moved onto watching the butter churner, even if it is a tad bit fast.
When the Mystery Machine parks in Oakhaven, the right window is empty.
Nearly have character is depicted with flesh colored sclera at some point in the movie.
The butter churner's face is randomly off-model every time she's seen from a distance.
From a distance, Velma and Ben while in the latter's car have little detail given. Velma's mouth is missing, as is Ben's jacket.
The customers standing outside the restaurant have no detail on their face, except for the few that have a line drawn across.
The puritan boy has modern-day sneakers.
Some notorious audio mismatch during the ending concert.
The sound of the mayor tapping on the door of Ben's study cuts right before his last one.
The way the young woman at night leaves after saying that maybe the Witch's Ghost would return the next day, it looks like it's in reverse of her turning to say something, only her dialogue removed.
The Hex Girls continously repeat that they have to go to sleep for the next day's concert. But they stay awake the entire movie since their introduction.
Velma is correct in stating that the modern-day word for "witch" comes from the word "wicca". However, "wicca" is a masculine Old English word that means "sorcerer", meaning that "witch" and "wicca" are technically synonyms.
When Jack says he has to make a trip to the market, Daphne's pupils are kind of bugged-out.
It's unclear what the corn husk dolls are doing on the tree stump, whether the villager is showing his or work or they're actually for sale. (Since there was already a gift shop there as well.)
For some reason Fred was not given blue irises in this film.
The man Scooby was disturbing (or harassing) must've had a big appetite as he had both a steak and a burger on the same plate.