In the Goonie house, when Mouth, Mike, and Brandon tell Chunk all his made up stories, Mouth tells him about when he said he ate his weight in pizza. Mouth says "Godfather's Pizza," but mouths "Pizza Hut." Pizza Hut refused to be mentioned in the movie, so the shot was overdubbed.
When the people in the car reveal themselves to be the Fratellis, Jake Fratelli starts to sing a song in Italian. When the camera turns to show Chunk screaming, you can still hear Jake Fratelli singing, yet you see him in the mirror and his mouth is closed.
While Mikey's Mom is showing Rosalita the house, she moves items around the room and gets a white paint-like substance on her right hand, which seems to come from one of the items. In the next shot, when they come back down the stairs, her hand is clean.
After the Fratellis pull the kids out on the deck of One-Eyed Willie's ship, Mouth has a mouth full of jewels. When Data shoots the suction cup dart at Mama Fratelli's gun and it starts to pull him toward her, Mouth's mouth is open and no jewels are there; in the next shot they are back.
While the boys are going through the attic, one of them knocks over a picture frame. The framed object is horizontal, but the hanging wire in the rear of the picture is for a picture that is framed vertically.
When the Fratellis are about to make everyone walk the plank aboard the Spanish ship, we see that Sloth is wearing boots. When the Fratelli brothers try to distract him by making him jump rope, there is a close-up of his feet in which he is shown wearing sneakers.
When Andy makes the first mistake on the bone piano, a huge hole appears and Mouth almost falls in. When she makes the second mistake, another hole appears and Brandon almost falls in, but the first hole has gone, and only reappears when the puzzle is solved.
Right before they found Chester Copperpot's remains, both Brand and Mouth were carrying different lanterns. In the next scene, Brand was carrying the lantern that Mouth had, with no time to switch lanterns.
At the beach, Francis Fratelli shifted the Jeep into 4LO (4x4 low range, very slow) The accelerating characteristics and highway speeds on the beach don't match a Jeep in 4LO. Shifting at that rate would be very jerky, and the jeep would likely not reach top speeds.
In the underground tunnels, Mama Fratelli never appears wet, even though they would have chased the Goonies through the waterfall at the wishing well and down the water slide tunnels to arrive at the ship.
After crossing the log over the river, as Data turns to make a rude gesture at the Fratellis, he is shown turning over his right shoulder. In the next shot, taken from the other direction, he turns over his left.
When Mrs. Walsh and Rosalita leave, the screen door doesn't close, and is left open when the Goonies go up to the attic. When the door bell rings, and they all go outside, they have to open the screen door to get outside.
When the Fratellis get back to the summer restaurant with the pizza it shows one of the Fratellis with a piece of cheese pizza in his mouth, yet Chunk and one of the Fratelli brothers repeatedly say that it is pepperoni pizza.
The logs in in the fireplace at the Fratelli's basement have burning embers on them. Then the embers are out when the Goonies enter through the secret hole. Then the embers are burning again when the Goonies tell Chunk to go get help.
When Troy's father and his associate drop off the foreclosure paperwork, you can hear rain, and they're both holding umbrellas. When Brandon walks down the sidewalk to them to pick up the paperwork, their umbrellas aren't wet. Neither is the car behind them, and neither Brandon or the paperwork gets wet.
When Rosalita asks for Mrs. Walsh's hands to pour the jewels from the marble bag into Mrs. Walsh's hands, Mrs. Walsh has very long, nicely painted, manicured fingernails. With the closeup which follows, the hand has shorter non-painted fingernails.
When Sloth breaks his chains to release himself, he rips them out of the wall. However, you can see from how he is chained that he is not only chained to the wall, but his hands are cuffed together. He does nothing to break the cuffs on his wrists yet when he rips the chains from the wall, the cuffs disappear.
The story takes place in Astoria, Oregon, but the beach scenes are clearly shot north of Cannon Beach, with Ecola Head in the near background and Haystack Rock farther back. Cannon Beach is 30 miles from Astoria, too far for the kids to reach by bicycle to in the time given. Aside from mountain logging roads, the only road connecting the two towns is Highway 101, which carries too much traffic for kids to ride on. Astoria is also about 10 miles east of the coast.
The final scene looks out to sea, with the sun in the background. However, the scene is supposed to take place in the morning, not late afternoon (as it would have to be with the sun in that spot over the Pacific Ocean on the West Coast).
When Chunk is on the phone with the sheriff and Sloth pulls out the cord that connects the receiver to the phone, a dial tone is heard on the sheriff's end. Unplugging that cord wouldn't have disconnected the call.
When Andy is playing the bone organ, as she gets ready to play the last chord, she gets stressed out and says, "I don't know if that's an A-sharp or B-flat!" Tonally, A-sharp and B-flat are the exact same note.
At one point, a newspaper headline that reads something like, "Fratelli's At It Again." This is grammatically incorrect. Since it is plural, not possessive, there should be no apostrophe; it should read "Fratellis."
At the end of the movie, Data tells the news reporters that the "octopus was really scary". This actually refers to a deleted scene, but there's nothing to indicate that he wouldn't just make stuff up and talk about something which (in the final version of the film) didn't happen. The octopus scene is included in the TV version of the movie.
The balloon used for the automatic gate changes color from red to pink. The change was most likely a result of the red balloon stretching to its popping point and the stretching made it whiter, meaning it would be pink.
When the kids ride to the restaurant, Chunk begs everyone for a Baby Ruth that he supposedly doesn't have. When he meets Sloth, he offers a Baby Ruth that he probably got from one of the others on their way over to the restaurant.
The incident with the plumbing makes the water dig a hole in the wall to reveal a secret entrance, however later in this new tunnel, the kids come across Chester Copperpot's skeleton. Since Copperpot had come that far, the wall should have already had its secret entrance opened. However, the basement with the (in-use) pipes was probably built after Copperpot went looking for the treasure.
When the pressure builds up and Troy is launched off the toilet by large amounts of water, you can easily see the platform he is sitting on and the pipe that pushes the platform up. Also, he is wearing red underwear on the toilet.
Chunk has a mole on his left upper lip. It's particularly obvious when he is reading about Chester Copperpot in the attic. But when he is thrown into the back of the black jeep, sees the dead body, and screams, the mole is on his right upper lip. It's Jeff Cohen's own mole, rather than a Hollywood mole, leading to the conclusion that the negative was flipped.
At the bone organ, when the kids look at the scores, one can see something like a line of single notes (a melody) with a few chords, but quite a long line. The girl just plays a few chords. Furthermore, at one point she says 'a c-sharp d' and nothing even similar to that is played by her.
When Sloth is watching TV before he breaks free, there's a shot of the TV where Sloth's face is reflected on the screen. His face is deformed, but the reflection of his face on the TV screen doesn't show his right eye deformed.
The goof items below may give away important plot points.
When the kids come across the dead explorer, they pull a baseball card from his wallet. The card is Lou Gehrig from the 1973 Topps collection. However, they mention that he has been down there dead since the 1930s.
The plumbing for a relatively modern building found in the lost tunnel indicates that someone had to have been there since Chester Copperpot was lost, thus the tunnel would not be unknown in the local area.