Revealing mistake: Right in the beginning car chase when Josh Brolin's name is on the screen the car runs under a tree and the shadow of that tree cast over the car shows the stuntman driving, not mama Fratelli. (00:03:00)
Revealing mistake: On Inferno's deck, when Data takes a stand against the Fratellis before he shoots the blue suction dart/string, the close-up of his utility belt is the same one seen at the start when he practices on the orange drum. Note the differences in the background and clothing/inventions under the coat. (01:31:50)
Revealing mistake: When the bats escape from the fireplace, it's obvious they are just black pieces of material.
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.
Revealing mistake: After Chunk smashes the statue and Mikey tries to put the penis back on it, we can see the statue is fake and is just made of rubber. When Mikey pushes the penis against the statue, the statue bends inwards slightly. (00:09:25)
Revealing mistake: When Stef blindsides Mama Fratelli with a punch to the face, you can see Mama Fratelli reach up and grab her face before the punch lands. (01:34:30)
Revealing mistake: When Mikey is on the balcony he turns towards Bran to hug him, and then Bran carries Mikey all the way to back of the balcony. During that whole time there are leaves falling from the sky. All the trees are outside of their picket fence and lower than their balcony roof. So they must have had crew on the roof throwing leaves down for the effect. (00:21:10 - 00:21:40)
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.