Continuity mistake: Chunk is tied to a chair when Jake and Francis leave him in the room with Sloth. When Chunk introduces himself to Sloth, the rope around Chunk's right shoulder has gone up, off the chair, but then manages to lower itself again, back over the chair in following shots. (01:04:05)
Continuity mistake: When Jake Fratelli searches through Chester Copperpot's wallet, it faces the opposite direction between shots - note the driver's license. (01:08:30)
Continuity mistake: Just as Data hands Mouth the lantern and Mikey tells him to translate, Mikey stands between Data and Mouth, but next shot as Mouth says, "Copper bones. Westward foams. Triple stones," Mouth is between the other two boys. (01:09:40)
Continuity mistake: When Brand says, "Why couldn't I have had a little sisterÂ…instead of that?" it cuts to Mikey as he raises his left arm to the 'triple stones', but next close-up it's his right arm that is raised. (01:10:20)
Continuity mistake: When Mikey turns the 'triple stones' and triggers the large ball, the ball is stained and dull-colored when it begins to roll, then changes to a clean, high-gloss brown as it continues on the track, but reverts back to its original coloring when it falls. (01:10:45)
Continuity mistake: After Andy kisses Mikey, when she tells Stef about it, her long hair is at her back, but in the close-ups her hair is in front of both shoulders, but next wideshot it's all behind again. (01:14:10)
Continuity mistake: In the cave, when Data does his 'slick shoes' there are metal plates attached to the back of his sneakers and strings which lead up the back of his pants, that instantly appear and disappear. (01:17:10)
Continuity mistake: When the Fratellis first catch up with the Goonies in the cave, in the close-up Data turns to his right to face the Fratellis, but next wideshot he is turned to his left as he gestures to them. The other kids' positions change between shots as well. (01:17:30)
Continuity mistake: In the cave, when Francis Fratelli begins to balance himself on the beam, in the close-up when he shouts, "Don't push, Jake," the flashlight is under his left armpit, but next wideshot he holds the flashlight in his right hand. (01:18:00)
Continuity mistake: When the kids first see the the skeleton bone keys, Stef and Andy are arm in arm with each other, but next shot facing the skeleton Stef is standing behind Andy. (01:18:15)
Continuity mistake: When Andy plays the final correct chord on the bone keys, the doorway opens and Brand rushes forward with nothing in his hands, as he grabs hold of the door's chain, but next close-up the lantern suddenly appears in his right hand. (01:22:10)
Continuity mistake: After the final correct bone keys are played, Andy is the last to cross, and in the close-up of her feet the map actually falls behind her into the hole, but it is back up in its proper place for Andy to make that last second grab for it. (01:22:25)
Continuity mistake: When the kids first see the Inferno, in the wideshot facing all of them, Brand stands between Stef and Mouth with Data and Mikey off to the side, but next shot facing the ship Brand is now at the other side hugging Mikey. (01:23:50)
Continuity mistake: When Mama Fratelli says, "Follow me," and begins to walk along the side wall, past the skeleton's bone keys, her body faces the skeleton as she holds a large flashlight in her left hand and the wall with her right hand. Next overhead shot she is turned around to face the wall and the flashlight has switched hands. (01:24:10)
Continuity mistake: When Mikey punches through the boards leading into the room with the treasure, you can see light coming through the opening. This could not be possible since there's a door on top of the opening that should block out any light. (01:27:25)
Continuity mistake: Before the 'bathroom' break, when Mikey holds up the map, the top of it is burned off and very few musical notes are actually there along its edge, but when they reach the skeleton's bone keys the top of the map is clean, with a musical score along the entire edge. (01:29:30)
Continuity mistake: Aboard the Inferno in One-Eyed Willy's quarters, when Brand says, "Don't know. Who cares?" he's holding a candlestick with a candle. When he fills his pockets with the riches in the previous and following close-ups, the candlestick style differs and it's loaded with melted wax. (01:30:25)
Continuity mistake: When Data shoots the blue suction dart at Mama Fratelli's gun, it leaves the stick behind still attached to his belt, but in the close-up of the gun the stick is attached to the suction cup and string. (01:31:50)
Continuity mistake: When Data shoots the blue suction dart at Mama Fratelli's gun, she drops the gun and when it falls below deck Jake's Sporto boot is seen on Mama's right (viewer's left), but in the previous and following shots Jake is standing to her left, beside Francis. (01:31:55)
Continuity mistake: On the deck of the Inferno, when Mama is pulling the pearls from Mouth's mouth, Francis is tying up Andy's hands with black rope. When Mama asks, "Is that all?" the color of the rope is off-white, but it then changes back to the black rope in the following shots. (01:32:30)
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.