There was a gag, created by the animators at Rhythm & Hues, where Scooby would turn into his cartoon version when he mistakenly drinks a potion. The gag was not in the script and was at one point chosen to replace a less-favored gag in which Scooby would turn into George W. Bush. In the end, Warner Brothers decided that they didn't want the audience to compare 2D Scooby to 3D Scooby, so they chose to have him turn into the Tasmanian Devil instead.
During filming outside the Vancouver Art Museum a boom camera zooming into the Mystery Machine after its arrival crashed into the back end of the vehicle, denting it and breaking the lens.
Velma's nameplate necklace reads 'Velmalicious'
The original Scooby-Doo episode dealing with the pterodactyl ghost featured a villain and motive that were quite different. The pterodactyl/hang glider costume was used to smuggle pirated music, with the small-town mayor behind the whole scheme.
In the high school clubhouse, Daphne has a dart throwing trophy.
When Velma is sitting in the backseat of the van and her leather outfit makes a farting noise, the line, "That was my outfit, I swear," was an ad-lib by Linda Cardellini.
When in Wickles mansion, the Gang finds a Celtic book with names written on the first page. Among the names are Harry Hausen (a nod to Ray Harryhausen, pioneer of stop-motion animation monsters), Werner Brovas (Warner Brothers), and Munster Mash.
At one point in the film, Scooby and Shaggy are pretending to sing into a toilet brush "microphone". The song they are actually singing is Strangers in the Night - Frank Sinatra's version featured the improvised scat lyrics, "Scoo-bee-doo-bee-doo", lyrics which then-CBS executive Fred Silverman chose as the replacement name of Scooby-Doo, in the original Scooby-Doo series. The original choice of name for Scooby was "Too Much", a popular catchphrase of the era.
The metal slide rule which Velma uses to calculate how to negate the effects of randamonium is, in fact, an E6-B flight calculator. The E6-B is an incredibly important tool for pilots to calculate wind velocities, air and ground speeds, fuel consumption, time en route, and aircraft course headings, amongst other things.