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.
Revealing mistake: Throughout the studio scene where Pee Wee is shot from the front being chased by security, the fact that his bike is on a rig can be seen by how rigid the bike is when he pedals it and it doesn't move side to side like it does when he's riding it freely in all the other shots.
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.
Revealing mistake: The entire snack bar cartoon sequence shot at the drive-in theater during the world premiere of "Pee-Wee's Big Adventure" is actually a montage of different shots patched together, and it almost looks completely seamless until you focus in on the car farthest right. Notice how the passengers change positions every time the shot changes on the drive-in screen. (01:21:00)
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)
Revealing mistake: In the scene where Pee-Wee is face to face with Professor Tanaka asking for Francis' whereabouts, the background behind Pee-Wee turns into an obvious painting on a set between shots. Notice how all sunlight and wind vanishes when he shouts "Where are they hosing him down?" (00:22:15)
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)
Factual error: When you see Large Marge's memorial in the diner it says that the day she died was January 11 and when Pee Wee goes to Texas and is running from Andy there is a Día de los Muertos parade going on. That holiday actually takes place on November 1st and 2nd, that's a major time difference of ten months. (00:44:05 - 00:59:30)
Visible crew/equipment: Near the end of Pee-Wee's chase scene at the Warner Bros. studios, he activates a launch mechanism on his bike and soars over a barb wire fence onto a roof. As he shouts "Geronimo," there is a crew member on the lower right hand side of the screen sporting a pair of sunglasses in front of a platform just staring towards the camera for a few seconds (best viewed on the matted widescreen DVD release). (01:17:05)
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.