Revealing mistake: In the bone organ scene, right after Andy plays the second correct note, when Data runs to the entrance the entire stone floor is intact, then it disappears again. (01:21:30)
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)
Continuity mistake: In the beginning scene of the cop calling out the inmates for their lunch, just as he calls "Hey Turkey." you can see the shadow of the supposedly hanged Jake Fratelli on the right wall. The shadow is totally inconsistent with the design of the cell and position Jake was hanging in. (00:00:45)
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: In the scene where they are playing the bone-organ to escape, the Fratellis walk across the beam then climb the rocks to get to the room where the Goonies are. In one of the rocks there is a tall metal post sticking up. A shot shows one Fratelli brother stick his hand on this post to pull himself up, but in the next shot the hand is gone and a moment later the Fratellis emerge from the water.
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: When the Fratellis leave the County Jail, the first police cruiser which makes the U-turn has a smooth chrome bumper with only a recessed license plate at the center, but when they make the first left turn, that squad car now has a chrome bumper with driving lights at each end and bumper guards on both sides of the license plate. It's funny how when they make the next right turn, the car style actually changes mid-turn, between shots - just before the second police cruiser joins the pursuit. (00:02:25)
Continuity mistake: When the back of the Fratelli's ORV is riddled with bullet holes, you can see they make a distinctive backwards "L" shape above the Jeep letters. Later, when Chunk examines the ORV, the bullets holes are now in different places than they were before, as well as two more holes in the license plate and the right brake light. Also, the license plate that is on the ORV when it is hit by the bullets, changes design as well. (00:02:45 - 00:30:30)