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)
Visible crew/equipment: Near the start, when Mikey unlocks the door, just as Mouth steps inside the house the actor's L-shape tape mark is visible on the porch. (00:06:20)
Visible crew/equipment: When Jake runs out of the County Jail, as the camera pans down when he shouts, "Francis, the lock," the moving boom's reflection is visible over the back door, and the camera's and cameraman's reflections are visible on the vehicle's surface, right behind Mama Fratelli. (00:01:30)
Visible crew/equipment: When Francis Fratelli walks across the beam he slips and does a flip. In the wideshot, we see the sudden appearance of a riveted platform affixed to the beam, extending from its left side, directly in front of Francis. (01:18:00)
Visible crew/equipment: When the Goonies are first climbing the ladder on the pirate ship to find one eyed Willy's gold, the second shot has a crew member waving his arm on the far left of the screen. (This is only visible in the widescreen version). (01:21:00)
Visible crew/equipment: In the shot of Mama Fratelli waiting outside for Jake in the ORV, you can see the reflection of some film equipment in the small triangle window next to her. (00:01:30)
Visible crew/equipment: At the Lighthouse Lounge, when Chunk opens the door and sees the bullet riddled ORV, Chunk's reflection on the back of the vehicle moves to the right, but there is another moving reflection to his left.
Visible crew/equipment: When Francis and Mama Fratelli carry the bagged corpse to the ORV, in the close-up the reflection of a crewmember, who moves his head, is visible on the surface of the black vehicle.
Visible crew/equipment: When Mr. Walsh rips up the foreclosure paperwork, the reflector screen is reflected in his glasses. (01:46:50)
Visible crew/equipment: When Sean finds that dirty old treasure map in the attic and tells them all the story about one-eyed Willy, behind Brandon and Mouth you can see some visible camera crew with a camera edging away from them in the shadows. (00:17:50)
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.