As the gang chase the villains through the mines, Shaggy, Scooby and Daphne stop briefly while Fred and Velma run on ahead. After a couple of scene changes, Fred and Daphne corner the villains in a cave, while Shaggy, Scooby and Velma arrive a bit later.
About ten minutes into the movie when the gang are in the La Serena spa in the hot tub, Mr. Hubley is seen without glasses but in another shot from the back side angle you can see that he is wearing glasses; the next front shot he again has no glasses.
Upon seeing the Phantosaur for the first time, Scooby's collar tag is all blue.
In Shaggy's hospital room, Velma goes from frowning concernedly to smiling in a close-up on Scooby-Doo, then back to frowning, in the space of three shots.
When Mr Hubley is doing the hypnosis on Shaggy, he drops his book. In the next few shots, it is nowhere to be seen.
A real ER doctor usually wouldn't take X-Rays unless Shaggy was either experiencing chest pains or was suspected of having fractured or broken bones.
When the gang is driving into town to chase the Velociraptors and the Phantosaur, Daphne's voice tells Fred to slow down but it's Velma's mouth that moves.
Unlike anyone who enters the hypnotism room, Winsor was not hypnotized during Hubley's session with Shaggy.
When the gang are in the mine showing Professor Svankmajer the pictures they took of the dinosaurs that attacked the town, she remarks that the larger Phantosaur might be what attacked her camp. Daphne's response indicates that the attack on Svankmayer's camp was news to the gang. Svankmayer then leads the gang out the only entrance to the mine directly into the destroyed camp. It is unclear how Daphne and the rest of the gang missed the wreckage when they entered the mine to talk to Svankmajer.
Velma identifies the tracks at the spa as Dromaeosaurus tracks, specifying the Mongolian species (Velociraptor mongoliensis). This species of Velociraptor was actually quite small. It was also feathered.