Factual error: In the scene immediately following Harry and Hermione's travel back through time, she tells him, "It's 7:30." The clock, however, is striking the bells for an hour, not a half-hour. (01:43:45)
Factual error: When hero boy and girl and Billy are on the runaway car at the north pole, they crash into the stopper at the end of the tracks. They are flung backwards when in reality, due to inertia, they should have been flung forward into the guard rail.
Factual error: When Professor Broom puts the old pieces of paper together, the text translates to "Graveyard 16", not "Sebastian Plackba 16".
Factual error: Flynn says that the chamber in the Mayan temple is "an exact replica of their great temple of Teotihuacan." But Teotihuacan was not a Mayan city, but rather the hub of a separate civilization (themselves called the Teotihuacan). It was in central Mexico, hundreds of miles from the Mayan area in the Yucatan Peninsula.
Factual error: After putting Jenna in the closet, everyone crowds together and plan to leave. One girl holds a diet coke can, which is obviously a more modern design, and not from 1980's. (00:10:30)
Factual error: As the Hood approaches central London in Thunderbird 2, they fly through Tower Bridge and over HMS Belfast, approaching from the East. However the onboard display in Thunderbird 1 shows TB2 approaching from the West, somewhere over Hammersmith.
Factual error: When the children jump off the remains of Aunt Josephine's house, they jump further than they'd be able to. The slanting floor, at least, would reduce the distance, plus they didn't take enough of a run up to jump the gap.
Factual error: On the map, Budapest is indicated to be just as large as Transylvania, or at least of the same size category. Apart from Budapest being only a city and Transylvania a pretty large county, Budapest (taking its 19th century size) is not more than 500 square kilometres while the Transylvanian region is circa 57000 square kilometres. (01:11:40)
Factual error: At one point in the film there is footage on the news of Mystery Inc's embarrassing attempt to stop the ghouls from stealing costumes. In particular, it focuses on Shaggy and Scooby being dragged across the table, etc. But look at the angle it's taken from: no one could have taken that.
Factual error: When Fat Albert and Reggie are racing around the school track, there are palm trees visible over Fat Albert's right shoulder in the background. The problem with that is the movie supposedly takes place in Philadelphia, PA.
Factual error: In the final credits, the song "Brazil" is credited to "Aro Barrosa". The composer's real name is Ary Barroso.
Factual error: In the scene where Mei is bathing in that small pool, you can see on her arm a the scar from her vaccination. As you might expect, they didn't have these vaccinations in the 1800s.