Revealing mistake: When the floor crumbles from under Mouth we see a shot looking up from the pit to him leaning back trying to keep his balance. If you look closely you can see him kneeling on the ground helping him to lean back further.
Revealing mistake: When Francis Fratelli is trying to pick up the gun as the Goonies are escaping from the organ, you can see the rocks shaking each time he drops the gun on the ground.
Other mistake: In the Summer Place scene, after Mama Fratelli sets down four glasses of "colored" water for the boys to drink. The next camera angle shows Mouth wiggling his glass in the air as he retorts, "We're supposed to drink this?", Mama snaps back, "It's wet isn't it? Drink it." If you look closely for 2 seconds you can see Corey Feldman is trying very hard to not smirk at this line, while struggling to stay in-character, as Mikey and Data say their next lines.
Factual error: The Goonies are from Astoria, but they ride their bikes to Cannon Beach; this is where the Lighthouse Lounge is, a distance of over 30 miles. When they descend in the tunnels below the lounge, they supposedly go under Astoria Country Club and Moss Garden. This would be impossible.
Continuity mistake: When Brand takes Data's sister's bike, there is a horn affixed to the handlebar which disappears when Troy pulls up beside Brand in his car and then reappears when Troy starts speeding holding Brand's arm.
Continuity mistake: When the Fratellis are trying to get information from Chunk, the amount of juice in the blender changes between shots.
Other mistake: When Chunk is reading the caption under Chester Copperpot's picture he says, "I have the key to One-Eyed Willy." The caption, however, only says that Chester has a key, but never says to what.
Factual error: When the Fratellis are getting away from the police at the beginning of the movie they go to the beach to blend in with the other 4x4s. Mama Fratelli tells Francis to put their Jeep into 4 wheel drive but you can see him put it into 4 wheel low. It's impossible to drive as fast as they did on the beach in 4 wheel low.
Continuity mistake: When Data is being dragged by the sticky dart in the opening sequence, the camera angle changes from in front to behind, and suddenly the distance between Data and the oil drum dramatically increases even though he is moving towards it.
Continuity mistake: When Sloth is trying to reach for the Baby Ruth, the candy bar's position and the way it faces changes between shots.
Character mistake: When looking at the newspaper about Chester Copperpot, the caption under his picture reads, "Reclusive scavenger claims, 'I have they key.'" It should read "I have the key."
Continuity mistake: When the Goonies are standing behind the waterfall in the cave underneath the wishing well, they've got dry hair. But just before Mikey walks through the waterfall, you can see that his hair is soaking wet already.
Factual error: There are a few problems with the suction cup that Data shot onto the metal drum. First off, suction cups don't stick to curved surfaces. Second, dirt and grime, which the drum obviously had, would not allow a suction cup to stick. In any case, it shouldn't have stuck.
Factual error: When the Goonies go below deck on the pirate ship, we can see water is leaking through the hatches on deck. In reality, the ship would've filled up with water and sunk in a matter of weeks, if not days, so there's no way on Earth that it lasted as long as portrayed in the film.
Other mistake: When Mikey is telling the story of One-Eyed Willy, something stuck to the lens of the camera is visible on his head. This is visible on the television airings but may or may not have been fixed for home media.
Factual error: When the Fratellis break Jake out of jail, Francis shoots a trail of gasoline on the ground with his pistol, which lights it. In reality, this wouldn't happen, more than likely the bullet would bounce of the ground or embed itself, but not cause any sparks (if it caused any, wouldn't be long or hot enough to ignite) to light the gas.
Continuity mistake: When Sloth kisses Chunk for sharing his chocolate, Chunk's cheek swaps from dirty to clean between shots.
Continuity mistake: The amount of jewels in the person's hand change position, size, and shape in the span of two shots near the end of the film when everyone is looking at them.
Continuity mistake: Before Chunk opens the Fratellis's door, Data looks at Mouth, and then turns his head at Chunk while smiling. A frame later, from a new angle, he is still looking at Chunk and repeating the previous movements.
Continuity mistake: When Jake Fratelli is in jail, the position of the sign on his chest changes between the first and second shot. The right tip is first touching his chin, and a frame later it's 15 cm below.
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.