When Jason finishes writing his story "Big Fat Liar", he staples the papers together, but when Marty picks it up in his limo, the papers are not stapled. Also, the writing of the title looks different from when we see Jason writing it (especially the "i" in "liar").
When Jason crashes into the limo you can clearly see the damaged bicycle. After Marty agrees to give Jason a lift and he goes to get into the limo, the bicycle is gone.
The shade of blue on Marty changes inconsistently throughout the movie.
When Kaylee gets stuck on the Velcro wall the position of her body, (most notably her height) continuously changes between shots.
After Marty's car is supposedly smashed by the monster truck the mag wheels are different when it is being towed.
Jason liberally applies a super glue-type product to the earpiece of Marty's cell phone hands-free set. Any type of super glue product should dry pretty quickly after it's applied. MArty finished swimming and took a shower as well as freaked out when he saw himself. By the time he stuck the ear piece into his ear, the glue should have at least been tacky if not dry. It would have been "easily" removable.
Jason and Kaylee are able to sneak in and spend the next few days in a movie studio warehouse with no security guards or cameras spotting them.
Jason and Kaylee were able to travel on an airplane alone. Minors would need a form of ID and would need an adult to accompany them for their flight.
When Marty swims in the dyed pool, all of his skin turns blue yet his bathing suit remains its original color.
When Marty tackles Jason on the roof for Mr. Funnybones, after Jason falls, the ground moves revealing a crash mat.
When Marty is upset that his car has been sabotaged and is banging away at the instruments, in the close up of his hands you can see he is wearing blue mechanical rubber gloves instead of the blue died skin.
Jason had Marty's stuffed monkey in the front pocket of his backpack and the pocket zipper was open after Jason takes the monkey out but before Marty attempts to chase Jason off the roof, it's still unzipped but when Jason runs from Marty and ends up jumping off the roof, the pocket zipper on his backpack is zipped. Jason never took off his backpack to zip it up and never had the time to do it.
When Janie's boyfriend arrives, he clearly switches off his engine and removes the keys, but the engine can still be heard. When he gets in the car again, the keys are in his hand but the engine is still running.
During the closing scene with Wolf as a clown, when he realizes the father is the owner of the monster truck who confronted him during an accident and destroyed his car, his ADR voice says "Oh, no", but his lips mouth "F*** me".
Crew members and lights are reflected in the blue dye bottle as Jason is pouring it into the pool.
After Jason and Kaylee have taken some time to look around at the warehouse that they use for their temporary home, Jason says that they'll hangout there until closing time and then go shopping. When he's saying this; behind him is a telephone booth. Reflected in it is a crew member in a white t-shirt reading some sort of newspaper or maybe the script to the movie. He is looking down at the pages then seemingly looking up at the actors as they say their lines. (Maybe he's the script supervisor or something.)
When Wolf realizes his car has been sabotaged (specifically where he finds that his brakes are connected to the car horn), his brakes clearly work as he stops his car (despite hearing the car horn when he hits the brakes) but immediately following we see he cannot stop the car.
Jason's parents knew he had his paper due but when Jason finished his homework. He realizes he has 15 minutes to hand it in. He struggles trying to get there and ends up taking his sister's old bike and ends up crashing into Marty's limo and Marty and his driver give Jason a ride. His parents should've been home and should've gave him a ride to hand it in.
In the classroom in the beginning, the boom mic is clearly visible for a significant amount of time.
The headline in Variety uses the word "Prez" to refer to the new president of the studio. Variety would always use "Prexy", not "Prez".