Revealing mistake: When all the kids are in the diner just before Chunk knocks over the water jug, Mikey starts to bang on the ground with a bar. When Brand stops him, Mikey calls him by his real name Josh. This is verified on the DVD by Sean Astin himself, in the commentary. (00:40:40)
Revealing mistake: At the start, when Data is being pulled towards the chained orange drum, due to the angle of the close-up, we see that the soles of Data's Nikes are not actually touching the ground (since there is a rolling mechanism under his feet). Despite the fact that Data is quite inventive, we see in the next shot there's nothing attached to Data's Nikes. (00:03:55)
Revealing mistake: During the police chase, when the Fratellis turn left in the close-up (just before the shot of Mouth's TV), sitting in the passenger seat instead of Francis we see a man who is taller, wears no glasses and is at least 25 years older than our Francis. Also note the man who is driving instead of the real beloved Mama Fratelli. (00:03:10)
Revealing mistake: When Chunk unknowingly flags down the ORV driven by the Fratelli brothers, as Francis drags Chunk to the back hatch there are cables that run from the ORV to the side of the road, off camera. These cables were not in the previous shot when the ORV first stopped.
Revealing mistake: Up in the attic, when Chunk walks over to Mikey (who wants Chunk to drop the frame), at that moment Data and Brand are alone, and while the two of them are looking at the plasma lamp Brand flicks the glass with his finger, and just as Data stares at Brand we can clearly hear Data say, "Don't touch it Josh!", which is Brand's real name. (Mikey does the same thing later at the lighthouse restaurant.)
Revealing mistake: When Troy is in the country club restroom, the toilet overflows and he gets pushed up to the ceiling, you can see that he is sitting on a platform. When the water shoots out, you can see the pole connected to the platform being raised up.
Revealing mistake: When the Fratellis get a visit from the bats out of the basement, two bats fly in front of Jake Fratelli and while they are flying in front of him you can clearly see their wires.
Revealing mistake: At the Astoria Country Club, when Troy first sits down in the stall and opens the magazine, behind him are at least nine columns of small patterned tiles. In his next close-up as he looks around, the wall behind him is completely different. Now there are only six columns of larger unpatterned tiles, with a long vertical gap between the tiles (where the grout should be) - which is the track for the mechanism to lift Troy in the following shots. (00:51:00)
Revealing mistake: Just as Mikey opens the front door for Data's entrance, the porch upper rail is seen right outside the doorway, with the chimes hanging from it. The problem here is the long wood plank at the top corner of the porch railing, that has been added to the decorative bracket that's seen in all other shots. (00:08:55)
Revealing mistake: When Sloth swings from the rope to grab Mouth and Stef, who are tied up on the plank, you can clearly see that the kids are fake dummies before and after Sloth grabs them. (On the DVD Commentary, Director Donner and Corey Feldman (Mouth) explain why 'dummies' were used.)
Revealing mistake: After dropping the frame and breaking the glass, in the close-up of Chunk's arm removing the map from the frame, the arm is larger and much older looking - note the wrinkled elbow and thin arm/hand, whereas Chunk's elbow has puckers at the joint and he has short and chubby arms/hands. (00:16:15)
Revealing mistake: In the bone organ scene, right after Andy plays the second correct note, when Data runs to the entrance the entire stone floor is intact, then it disappears again. (01:21:30)
Revealing mistake: When Data falls into the hole and is saved by his Pinchers of Peril, which is attached through his left sleeve, the real stunt cable behind him is visible. (01:11:15)
Revealing mistake: When Brand finds the skeleton key in the dirt, he holds it up as Mouth wipes the dirt off the three holes. It's actually quite funny seeing what is supposed to be Mouth's hands in the close-up, with its female manicured fingernails. (00:55:40)
Revealing mistake: In the scene in the cave where Brand pulls back the rock and the bats fly out, there is a close-up of Mouth with bats flying in front of his face. You can clearly see the wires attached to the bats.
Revealing mistake: When the Fratelli brothers pick up Chunk on the road, the mole on Chunk's face switches sides when he is with the dead guy in the back. The shot is flipped. (00:49:40)
Revealing mistake: When all of the Goonie kids run upstairs to the attic, they rush past the camera, and you can see the image wobble slightly, as if one of them jostled the cameraman.
Revealing mistake: When Chunk opens the freezer in the Fratelli hideout to get the ice cream, if you look closely at the old dead man he moves his eyes several times between standing upright and falling over, and when he and Chunk are in the freezer together.
Revealing mistake: As the dead guy falls out the freezer, he is seen blinking.
Revealing mistake: When Brand moves the rock and hundreds of bats fly, note that the blatant fake rock has a chunk of painting missing, revealing the white material underneath.
Answer: According to Mikey and Mr. Walsh, one of his crewmen must have taken the map and fled when One Eyed Willie was murdering his crew. This is substantiated in the novelization.