Around one hour into the film, when David and his gang attack a group of people while Michael watches on, one of the victims is the punk with a gray stripe in his hair who was killed earlier in the film.
When David is first meeting Michael on the Boardwalk, there is a wide shot in which David is clearly saying something to Star - though no audio can be heard. In the next shot of a close up of David, you can hear and see him saying his line.
At the beginning of the movie when Michael, Lucy and Sam stop at the gas station, Michael unloads his bike from the back of the trailer. Then, during the montage of locals from Santa Carla there is a shot of the three of them in the car again, and then shortly after they pull up at Grampa's and Michael is riding his bike.
When Sam is first introduced reading the vampire comic, his dog Nanook is on the left side of the bed, but then after when they show the scene were Sam grabs the beaver art, Nanook appeared to be on the right side of the bed.
The couple in the car reading comics towards the beginning (after stealing a comic from the store), are sat with the comics on the shelf behind them when they hear a noise from outside. Then, when the roof is taken off the car by the vampires and you see the shot from above, they are now sat with all the comics in front of them.
Just before Michael has his first Vampiric episode, he opens the pouring spout only on the carton of milk with Laddie's picture. Struck by sudden pain, he falls to his knees in front of the refrigerator and spills it. It lands fully open and facing more or less toward the fridge. When Lucy enters the kitchen and discovers the carton later, it's back to pouring spout only and facing directly toward the doorway.
In the comic book store, the Frog brothers chase the Surf Nazi's out of the store. After they leave, Sam looks down at the comic they have given him. We can see Alan standing in the shot, exactly where he was before he left.
The credits at the end give credit to the poster hanging on the wall in Sam's room as a still from The Breakfast Club. In fact, this picture of Molly Ringwald in a dark blue shirt sitting in a classroom is not from The Breakfast Club, but instead, from Sixteen Candles.
Sam is supposed to be a serious comic book collector. However, during his first encounter with the Frog brothers in the comic book shop, he picks up several comics at the middle of the spine with enough force to bend the spine of the book, the first one pretty severely. Any comic book collector knows that this damages the book and would never pick one up that way. Also, a comic book shop owner would likely go ballistic if a customer handled books this way, or at the very least not let them handle any more books.
When Sam wears the concealed garlic necklace to bed with his mother, she exclaims that he smells like garlic. However, the garlic around his neck is still whole in bulbs and would therefore have a very weak scent, if any. It is not until garlic is peeled or crushed that its smell becomes apparent.
The family is moving to Santa Carla, CA from (presumably)Phoenix, AZ. However in the main titles, as they're driving, the coastline is on their right which would mean they are driving south. If they're driving from Arizona to (again, presumably) Central California , they would never be driving south.
Before Star gets on David's motorcycle to go to the cave, she isn't wearing a coat. During the motorcycle processional to the cave, she suddenly appears wearing one. However, she can be seen putting on a coat just before this sequence.
When Sam enters Michael's room after his first encounter with the Lost Boys, Sam opens the blinds to let light in. A second later, light starts pouring in from the bottom right corner of the screen from a mistimed light.
As the wife of the Board Walk security guard posts her missing persons poster, another poster is visible which advertises an event at the Santa Cruz County Fair Grounds. For the film, Santa Cruz was renamed Santa Carla to avoid associations with the city and the film's gang-related themes.
The goof items below may give away important plot points.
When the Frog brothers and Sam stake one of the vampires, some vampire ooze clearly gets onto the back of Sam's sweater making a big red stain and is there in the next scene. However, when Sam goes into the movie store to warn his mother about the vampires, the big red stain on the back of his sweater is gone.