Continuity mistake: At the start, when Data practices with the blue suction dart, in the close-up as the dart flies out we can see the mechanisms inside Data's invention. When it cuts to a tighter close-up, suddenly there is a spinning spool welded inside, which was not in the previous shot, that is retracting the orange string. (00:03:50)
Continuity mistake: In the opening scene where Data is using his sticky dart on his belt and being dragged towards the full bin, it changes to being empty just before being pulled in! (00:03:50)
Continuity mistake: When Andy begins to lose it in the tunnel, Brand holds one lit lantern at the head of the line and Mouth holds another lit lantern at the back of the line (Mikey holds an unlit lantern). Next shot the lit lanterns have switched, just as they reach Chester Copperpot and Andy screams. Then in the next wideshot before it pans to the skeleton, the lantern Brand holds up switches yet again. (00:53:15)
Other mistake: In the pirate ship scene, when the large boulder is falling from the ceiling of the cave into the water, its splash is far too small.
Continuity mistake: When Brand tells the others that the $50 bills are fake, Stef takes the newspaper with the Fratelli family mugshots off the post, from over the telephone. Then when Chunk gets the ice cream out of the freezer, the newspaper is back up on the post, but when the kids lift the dead body off the floor, the newspaper is missing from the post. Finally, in the shot just before Chunk shouts, "Guys, I'm stuck with the stiff," as the kids run into the fireplace, the tired newspaper is now lying on the printing press. (00:42:45 - 00:45:15)
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.
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)
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)
Factual error: Two of the huge rocks which plummet from the roof of the cave hit the water and then bob to the surface again. Pumice is the only rock which floats on water, but this rock is white and pumice is grey, and pumice is too light and porous to form cave walls anyway.
Other mistake: At the end, Mouth goes up to Stef and thanks her for offering to save his life. During the movie, however, Stef never offers to save his life. It is explained somewhere that in one of the deleted scenes, when Stef and Mouth are on the plank she offers to share her breath with him so they can both breathe under water.
Audio problem: Many of the gunshots during the chase scene are off cue with the police officers' shooting. (00:02:40)
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)
Factual error: When Mouth flattens the tires on Brand's bike, all he does to let the air out is take the valve caps off. There's actually a valve in the valve stem that needs to be depressed to let the air out. The cap is just there to keep dirt out of the valve, simply taking it off wouldn't let the air out.
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)