Fred and Barney's test slabs are (not) chipped and broken.
During the opening scene, the roof of Fred's car is shorter than it is for the rest of the movie. (See trivia.)
When Fred is eating with Wilma and Betty in the Cavern on the Green, the bottle in the bucket alternates from being straight or upside down. It even disappears in some shots.
When Fred stands up to talk about the model houses, there is a close-up of him. In the next shot his hair and the lighting of the scene are completely different from the previous shot.
Fred's ears/hat when he and Barney are drinking beside the grill.
Since the villain's plan called for finding a patsy to pin the blame on, logically they should have "promoted" the employee who scored the *lowest* on the test instead of the highest. They wanted the dumbest, most gullible person possible since he presumably would have been the least likely to figure out exactly what was going on. While looking at the test scores, Cliff expresses his knowledge of Fred being a "dunce and witless" and may very likely know that his test had to have been switch which someone else. They also should have terminated the person with the *highest* score, for the opposite reason, which they did after checking the scores and assumed that Barney had to be the one that Fred had switched tests with.
When Fred is encouraged by Vandercave to splurge on luxuries commensurate with his promotion to vice-president, he, among other things, adds a second floor to his house. Yet in the final scene of the film when Fred pounds on his front door and shouts to be let in after the cat has thrown him out, the additional floor nowhere to be seen. However the film is presented as a "film in a film", so none of it (including the extension to the house) happened to the characters in their world - only on a movie screen they were watching. That is to say, the house was never extended.
Fred asks Betty if she wants to dance right after the BC-52s finish their set and say "Good night". However, Cavern on the Green could have another band appearing after the BC-52's, just as its real life counter part (Tavern on the Green) was once frequented by musicians.
The gigantic stone on the catapult is wobbling like it has no weight and in the wide shot the wire attached to it is also visible.
When Bamm-Bamm is pushing Pebbles on the swing, the swing beam between the swing chains can be seen spinning along with her as she goes around full 360.
Wilma's fingers squeeze the briefcase Barney gives Fred at the party.
The wheels on the Flintstone's car are clearly just painted modern steel oil drums. Evidenced by the two thin bulges in the middle of the wheels.
When Fred pulls up in front of the House to pick Wilma and Pebbles up in the opening montage he is wearing shoes.
Immediately after the test as Barney goes to collect Fred's test he is wearing sandals.
At the end of the movie, as everyone is leaving the drive-in movie theater, a dinosaur follows the Flintstones' car and the crew can be seen working the dinosaur underneath. As well as the rig holding up the dinosaur's neck.
Depending on the aspect ratio there is a cameraman and equipment is full visible as Fred is hiding from the police.
If Bamm-Bamm is supposed to be the world's strongest kid, how did he allow himself and Pebbles to be tied up and captured? Couldn't he have knocked out Vandercave, or at the very least, broken the rope he was tied up with?
Fred is about to be hanged by the laid off quarry Men workers, then Barney turns up to sell snow cones how come none of the quarry Men recognize Barney? They have worked together and some of them are on the same bowling team.
When Fred and Barney are about to be hanged Wilma and Betty can be seen racing towards them in a car, in that instant Betty calls Wilma 'Willa'