Continuity mistake: On the deck of the Inferno, when Francis is tying up Andy's hands in the tight close-up, his gun holster is gone. (01:32:35)
Continuity mistake: When you first see Andy's hands being tied, you can see that they are tied fairly tight. Right before she goes off the plank, you'll see that the rope is barely around one wrist. In the next shot as she is going into the water, you can see her holding her elbows with both her hands. Then when Brand rescues her the rope is secure again. (01:32:40)
Continuity mistake: On the Inferno's deck, after Mouth spits out the jewels from his mouth, when Andy calls Mama, "You gross old witch," Francis is tying up Andy's hands and his sword is held between his legs, but in the next shot Francis is behind Stef and the sword instantly appears in his hand held high. (01:32:45)
Continuity mistake: On the beach, when Mr. and Mrs. Walsh leave the van and then rush to Mikey and Brand, Mikey's knit hat is pulled down low over his ears, but next shot it is folded up above his ears, though he never touches it. (01:41:55)
Continuity mistake: At the end, when the Fratellis show up on the beach, Chunk and the others run over to Sloth to protect him and Chunk stands on a large boulder. The ground is rocky and the sand is brownish. When Chunk tells Sloth that he'll live with him, in the overhead close-up Chunk is now shorter than Sloth and the ground is pristine off-white sand. (01:44:10)
Continuity mistake: On the beach, when Mikey tells his father, "We had our hand on the future, but we blew itÂ…," in the close-up the brown blanket is only on Mikey's left shoulder, but in the previous and following shots the blanket is snugly around both shoulders. (01:45:25)
Continuity mistake: When Mr. Walsh has the paper on Mr. Perkins back, the top paper reads "final notice" when Mouth turns to stop him from signing, but when it cuts to the close-up, that "final notice" top sheet is actually gone. (01:46:10)
Continuity mistake: At the very end on the beach, Chunk is wearing a knit hat, but Mouth is not (he took his off earlier). Then in the shot looking up at the Goonies, who are circled around the hand holding the jewels, Mouth is now wearing a knit hat and Chunk's hat has vanished, but next shot they've switched back again. (01:46:30)
Continuity mistake: When Rosalita (black coat) pours the jewels into Mrs. Walsh's (beige coat) hands in the first close-up, the hand holding the jewels has long nails with colored nail polish. It cuts to a close-up of the Goonies looking down on that hand, and then cuts to a tighter close-up of just the hand holding the jewels, but now there is no nail polish on the thumbnail and the nail is shorter. (01:46:40)
Continuity mistake: After Mr. Walsh tears up the paperwork, when the reporter steps forward to ask if the jewels are real, Mouth stands right in front of him facing the other kids, but next shot Mouth instantly stands behind the kids, facing the reporter. This continues to go back and forth. (01:47:00)
Continuity mistake: When the Inferno sails past everyone on the beach, in the close-up of Mikey blowing a kiss and saying thanks, he has a blanket wrapped around him, but next wideshot the blanket is on the rocks, at his legs. (01:48:10)
Continuity mistake: On the beach, when Mr. Walsh is tearing up the contract we see the bits of torn paper, but when he tosses them in the air there are many more pieces of torn paper up there.
Continuity mistake: On the Inferno, when Sloth swings in and rescues Stef and Mouth from the gangplank, as he drops them on deck Sloth wears all black high-tops with black laces, but in the previous and following shots he wears his usual black high-tops with white soles and laces.
Continuity mistake: When the kids light the two lanterns they find in the pipe room, they stay lit somehow, even though the lanterns get wet in the well.
Continuity mistake: Chunk breaks the glass on the frame and then he and Mikey clear away much of the broken glass from it. When there is another view of the picture all the glass is still on it.
Continuity mistake: When Sloth pulls the chains out of the wall, he picks up the Baby Ruth and there are no shackles around his wrists. He didn't break them, he only broke the chain at the wall.
Continuity mistake: When Data crashes through the screen door, as Chunk begins to fall backward with the statue, the pothos plant that falls off the table is in a black plastic container, but that pothos plant was actually in a large white ceramic pot in previous shots.
Continuity mistake: Whenever Data uses his boxing glove device, it creates a rather large bulge in the side of his jacket. However, this bulge isn't present through most of the movie, it just magically appears whenever Data uses the boxing glove.
Continuity mistake: In the scene where the kids are crossing the wooden bridge near the waterfall, Data is seen holding a lantern. After he does his "slick shoes" routine, the lantern has disappeared.
Continuity mistake: At the end when everyone jumps off the gangplank to escape, between three consecutive shots we see Data and Chunk jump off twice.
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.