Visible crew/equipment: When Pee-Wee is riding the bull, the announcer finishes saying "He's going for a new world record", and at the bottom, middle/left you can see that Pee-Wee is not riding an actual bull. If you have a quick eye, you can see he's riding a mechanical bull like the one from the movie Urban Cowboy. (01:00:50)
Revealing mistake: When Mickey drops off Pee Wee in the middle of nowhere he hears animal sounds all around, so he reaches for his headlight glasses and puts them on. All the animals except for a few small critters like raccoons are all fake. (00:40:55)
Other mistake: As the automated setup makes breakfast, it makes a total of seven pancakes (the two that end up on his plate, and five stuck on the ceiling). Trouble is that was only enough batter for one pancake, and no refilling device.
Continuity mistake: As the Rube Goldberg type setup works, the gold cherub statue pours batter in the pan the Lincoln statue is holding. When the camera angle changes, the cherub starts to pour the batter again.
Other mistake: In the beginning, as Pee-Wee waits for the crown in his dream, a bell starts ringing, and everyone leaves, leaving him alone. After all the photographers are gone, there is one more flash from a camera before the transition to his room.
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: Just before walking out of Chuck's Bike-O-Rama, Pee-wee grabs his custom-made horn from Dottie. At first he's holding it by the shiny steel part, but between shots his hand jumps to the base. (00:18:20)
Continuity mistake: In the studio scene, the tow rope from the boat flies through the area and attaches to the antlers of Santa's reindeer to start dragging the sleigh. In the subsequent shots of the boat and sleigh, the tow rope is attached firmly to a bar between the reindeer.
Continuity mistake: During Pee-Wee's breakfast, an oversized butter knife on the kitchen table changes positions in alternating shots. Sometimes the handle is hanging over the table's edge and other times it's not. (00:06:45)
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)
Other mistake: Five pancakes are made and shot onto the kitchen ceiling, yet only one is on Pee-Wee's plate.
Suggested correction: I think it's reasonable to presume that one simply fell down onto the plate while the others remained stuck to the ceiling.
Continuity mistake: During the scenes where Pee-Wee is riding with Large Marge, a quick exterior shot of the passenger side of the truck shows Large Marge's rig towing a trailer with horizontal ribbing. After dropping Pee-Wee off at the truck stop, her trailer changes to one with vertical ribbing.
Continuity mistake: Right after Pee Wee gets thrown off the bull, Andy jumps in. The bull starts to chase him. He jumps over the fence and there is a edit or cut before the bull does. You can see people in the stands arms change position. (01:01:15)
Continuity mistake: When Mario reaches for a red boomerang bow tie in his breast pocket, the angle at which he holds it changes between frames. (00:16:05)
Continuity mistake: When Pee-wee dives into the pool after Francis, some of the toy boats reposition themselves between shots. (00:23:40)
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 Mickey has to stop his car for the officer, he shifts into park and sits rigidly, facing the windshield. From the next angle he's facing right instead. (00:36:25)