Right after they begin the search for Velma, she is seen right behind Freddy looking for herself.
The Three Stooges are with the kids as they examine Tyrone, but mysteriously disappear when Amos Crunch confronts the gang as trespassers, and aren't seen again until the next scene.
When the Stooges meet the gunslinger in the wax museum, he is clean-shaven and has a rounded face. In all later appearances, he has a mustache and a thin face.
The mechanical T-Rex looks like a realistic animal when it was seen on a cliff, but then looks like an enormous robotic toy when they encountered it.
The dummies are parallel to the window when viewed from outside, but perpendicular to the window when Shaggy and Scooby go inside.
While requesting help from Shaggy and Scooby, Fred loses his lower body.
As Fred and Daphne are walking in the desert, only Daphne is leaving footprints.
Right before the T-Rex digs into the mine, one of its hands is missing.
When Scooby was telling the gang about the gator, Shaggy's lips were moving when Velma's voice was heard saying "You mean" before Velma's lips were moving.
It's clearly Moe's voice commanding to 'hit the breaks' in the mine cars with Curly's voice responding, but the animation has Moe in front doing the breaking and lipping Curly's response. (In other words, the animators mixed up Moe and Curly Joe.)
While searching for Velma, Daphne and Fred get lost in the desert. However, when the Indian appears, screaming and yelling while thunder strikes in the behind him, Daphne and Fred are shown to have somehow returned to the amusement park, with no explanation of how they got back.
When Moe first talks about Tyrone the T-Rex model, he says Tyrone is a *plastic* model. But when they go to see it, Velma comments that there is not a single break in the *plaster.*