Continuity mistake: When Pee Wee walks up to the bums at the drive in, the soda falls over in the holder in his right arm. When he steps in to give them their snow cones, it's instantly standing again only to see it fallen over again when he watches the fight scene with the ninjas on screen.
Continuity mistake: After throwing the candy to the bikers, Pee Wee is holding a box of Milk Duds and a candy bar. After he watches himself in the movie, the candy bar disappears then reappears behind the Milk Duds between shots. Then in the next shot of him skipping towards Dottie - all of the candy disappears completely.
Continuity mistake: When Pee-Wee is wandering through the Warner Bros. lot in search of Kevin Morton, he asks a feminine-toned crew member for help. The member grabs his helmet with the left hand, saying "Gee I don't know." But in the next shot he reaches for the helmet all over again. (01:09:50)
Continuity mistake: At the police station when Sgt. Hunter tells Pee-Wee that hundreds of bikes are stolen every month and very few are recovered, her hands change positions between shots. Initially she's holding them together while talking to Pee-Wee, but then her right hand is waving a blue pen around. (00:21:20)
Continuity mistake: During the Warner Bros. chase sequence, Pee-Wee blasts through a studio that's filming a beach-themed movie. Upon exiting into the alley - where only a couple of idle trucks are present - he's pursued by a security guard driving a boat with two skiers in tow. But in the next shot, a station wagon and three actors emerge in the alley from out of nowhere. (01:14:20)
Continuity mistake: When Pee-Wee is in the car with Mickey, some shots are shown from Mickey's point of view and you can see the background behind Pee-Wee. If you look carefully, you can see that in the background there is a road that comes into the main road they are driving on. This smaller road appears twice, as if they have not moved anywhere.
Continuity mistake: After Mickey and Pee-Wee evade the highway patrolman, Mickey takes a good look at Pee-Wee in the outfit and smiles. Before the scene cuts away, you can see how the convertible is missing its rear-view mirror. Soon Pee-Wee sends the car over a cliff's ledge and, as they're screaming together on the way down, a rear-view mirror is hanging from the windshield all of a sudden. But once the car hits ground, the mirror is no longer there. (00:37:40 - 00:39:00)