Continuity mistake: In the breakfast scene, one shot shows pancake dough being poured onto a frying pan. In next shot, when Pee-Wee goes to the bathroom, the dough is poured again. (00:04:40)
Continuity mistake: When Pee-Wee is walking away from his house with his bike, you can see two lawn gnomes behind him, next to his house. When he sees Francis, the lawn gnomes have mysteriously disappeared.
Continuity mistake: After Pee-Wee loses the Warner Bros. security crew on his tail, he sees a burning pet shop and decides to rescue the animals inside. Take a look at the early '80s red and black Chevy Suburban parked by the entrance. Whenever Pee-Wee runs outside, the amount of sunlight cast on the vehicle changes (sometimes lots of light, very little light or none at all) as though the scene were filmed at different parts of the day, then pieced together. (01:17:25)
Continuity mistake: Early in the Warner Bros. studio chase sequence we see a team of security guards in pursuit of Pee-wee. Somehow the guard in front switches from using a golf cart to a bicycle, all within a few brief cuts. This is the same guard who pulled the right handle from Pee-wee's bike moments ago. (01:13:05)
Deliberate mistake: In the scene where Pee Wee is dreaming after his crash, the crane that is going to pick up his bike misses the bike completely and then is shown in the air as if it actually had grabbed it. (01:07:50)
Continuity mistake: When Pee-Wee is on the roadside trying to hitch a ride to Texas, the sun casts a shadow behind him which is mostly parallel to the road. But in the subsequent shots of oncoming cars, the sun is casting a long shadow on each one's passenger side - obviously implying a different time of day. (00:33:00)
Continuity mistake: In the scene where Andy chases Pee-wee down with a dinosaur bone, we can see Simone in the background flailing her arms and screaming Andy's name. At first she's walking towards a nearby staircase on the dinosaur's left side, but between cuts she quickly repositions and is now standing in front of the dinosaur's large foot instead. (00:49:25)
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.