Continuity mistake: After Chunk walks in, when Mouth and Mikey kneel in front of the aquarium Mouth's white sock is visible, but when Chunk places the statue on the edge of the table and it falls, we see that Mouth's sock has vanished. (00:08:10)
Visible crew/equipment: After doing the Truffle Shuffle, when Chunk walks into the Walsh's house, the reflection of crew/equipment is visible in the window to the right. (00:08:15)
Continuity mistake: When Data places the cassette into the tapedeck and grabs hold of the bar on the zip-line, his palms face him as he takes off, but next shot as he slides down his palms face out. (00:08:50)
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)
Continuity mistake: When Data crashes through the screen door, sending Chunk to the floor with the statue, in the first shot there is a long bright stream of sunlight shining on the carpet, between Chunk and the stereo which disappears in the next shot. (00:08:55)
Continuity mistake: After Data breaks through the screen door and causes the pile up, the potted plant that was on the table is already lying on the floor in the next shot of Chunk catching the statue, even before it falls and hits the floor. (00:09:00)
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)
Continuity mistake: When Brand hangs upside down from the bar, we can see that the kitchen table and four chairs are right in front of the kitchen window. But when Mikey unrolls the map in the kitchen, Chunk, Data, Mikey and Mouth are standing directly in front of that kitchen window, which is completely impossible to do. (00:09:40 - 00:22:35)
Continuity mistake: When Mrs. Walsh shows Rosalita the house, the attic door is open and we see that it opens at the left, with the wallpapered wall behind it and nothing in front of it except the banister. When Brand opens that door and the boys rush up, we see the wallpapered wall behind it, only this time the attic door opens at the right. (00:11:25 - 00:13:50)
Continuity mistake: When Mrs. Walsh, Rosalita and Mouth go back downstairs, after Mouth's interesting interpreter skills, in the first shot Rosalita holds her umbrella in her left hand upside down, but next shot it's in her right arm, right-side up. (00:12:25)
Continuity mistake: When Mouth returns downstairs with Rosalita and Mikey's mom, Chunk already has the statue he broke turned away so no one will see, in the next shot he turns the statue away from everyone's view. (00:12:25)
Continuity mistake: When Chunk and Rosalita are eyeballing each other regarding the statue, there are colored curtains and sheer white curtains hanging from white rods on the two windows behind Chunk (behind the recliner). When Mikey unrolls the map in his kitchen, through the doorway we see that the sheer curtains are gone and now there are shades behind the colored curtains. (00:12:30 - 00:22:25)
Continuity mistake: When Mrs. Walsh asks, "What is that?" pointing to the mess on the table, the bowl is filled with chips in the close-up, but when she walks out with Rosalita the bowl is nearly empty. (00:13:00)
Continuity mistake: In the shot of the Goonies running to the attic upstairs, you can plainly see that it is not raining or stormy outside. When they enter the attic (barely seconds later), it's already raining outside along with the thunder and lightning. (00:13:40)
Continuity mistake: When the boys reach the attic Brand fixes the flickering lightbulb. Then they show a shot of Mikey and Mouth and you see Brand fixing the flickering lightbulb again in the background. (00:14:04)
Continuity mistake: In the attic scene, right when Mikey scolds Mouth for ruining the painting, you can see Brand standing next to the plasma lamp which is turned off. In the next shot of Brand reading the book, the plasma lamp is on. (00:14:50)
Continuity mistake: When Chunk drops the frame with the map, in the shot looking down at the frame lying on the floor, there are five narrow planks of wood flooring under the frame, but next shot there are three wide planks. (00:16:10)
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)
Continuity mistake: The design on the face of the treasure map and its two holes change, from the scene where the Goonies are in the attic to when they are downstairs again (i.e. it has a red stripe across it at first sight that disappears). (00:16:35 - 00:22:25)
Other mistake: Up in the Walsh's attic, in three shots of Mikey as he continues to say, "Then he loaded it all up onto his ship and he sailed away into the sunset..." there is something black hanging down from the top of the screen that stays put as the camera pans in closer to Mikey's face. It disappears, then reappears when he says, "Trapped." (00:17:20)
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.