As the gang and the Globetrotters start to drive off to Uncle Nat's house, the Globetrotters' dog appears briefly, but since he doesn't appear again, it's more than likely an animation mistake. Their bus driver, Granny, was also briefly seen.
In the final scene, Scooby's sclera are brown instead of white.
Fred states that no one has ever photographed the Loch Ness Monster, but the entire Nessie craze began with the "Surgeon's Photograph" in 1934, which has become ubiquitous in popular culture.
Freddy refers to the ghost of Paul Revere as the one with the lantern, even though the Minuteman Ghost holds the lantern in most scenes.
It seems odd that the conspiracy would portray characters from opposing sides of the American Revolution. It makes their illusion less credible.