In the first Flintstones movie, Fred stated that he met Wilma after she cleaned him off in an eating contest. In this movie, they met at a carnival after a date swap when Fred met Betty at a fast food restaurant, and Betty introduced Wilma as a date for Barney.
In the first movie Wilma rips off her pearl necklace after a fight with Fred, saying that she doesn't need it, as it was a present from Fred. However in this movie it is stated that the necklace was given to Wilma by her father.
When Fred shows Wilma how to bowl, the ball breaks in half before it hits the ground.
In the party scene, after Dino runs across the table and makes a mess, Wilma's mother's hair has some debris in it. She wipes it off with her hand, then in the next scene a piece is back, she picks it off, and in the next scene, more debris is back in her hair.
After Wilma takes a short walk and is stopped by Chip, the elevator door closes, then reopens when a lady pushes a button, a few seconds later, someone else pushes the button and it opens, not taking any time to move from the floor it would have gone to, and there's no one inside.
When the mother discovers Wilma living with Betty, the shadows of crew and equipment are visible along the wall.
When the policemen and guards chase Fred and Barney backstage and trip over the dropped bowling pins a crew member is fully visible before cutting to the next scene.
During the movie it is stated that Fred and Barney are the only one who can see Gazoo. However at the end Dino is licking Gazoo and he says to him that "it will never work out", which made Dino sad. That means that Dino was able to see Gazoo as well.