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.
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.
When Mouth is translating in Spanish for Rosalita, he says, "La rapidez está en el cajón de abajo," which the captions translate as "speed is in the bottom drawer" referring to the drug methamphetamine. However, in Spanish, the word "rapidez" literally means velocity or speed, and it is not used to refer to the drug.
When Brand starts to go after the rest of the Goonies on his bike, Mrs. Walsh says that if he was not back with the rest, she would commit "Harri-Krishna," after which Brand (incorrectly) corrects by saying, "It's Hari-Kari, Mom." What Brand meant to say was "Hara-Kiri," and not "Hari-Kari."
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.
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.
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.
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.
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.
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.
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.
At the end of the movie when the Goonies are on the beach talking to their parents you hear someone say, "The worst part was the octopus." There was scene in which a octopus attacks the Goonies but the scene was cut in the final cut.
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.
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.
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.
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 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.
On the porch after the foreclosure papers have been delivered, the background shows trees in full bloom/growth with no end of season coloration, yet the wind and rain are blowing many fall colored leaves onto the porch.
The treasure map that is first looked at in the attic has holes and red spots on it (matching the deleted scenes in the convenience store and outside the restaurant) but the one that Mikey opens in the kitchen for all the boys to look at (right after the attic scene) is much more intact and clean.
In the restaurant basement Stef finds a newspaper on a pillar that tells about the Fratellis and the others look at it. A moment later when the freezer door is opened, the newspaper is back where it was found without any indication that it has been put back.
After being in the pipe from, their hair keeps going from wet to dry. For example, Mikey's hair is dry when he tells Andy to hold his hand, then wet in the next shot when he sees the waterfall and exclaims "Oh, wow!" Next, the first time the kids are seen through the waterfall his hair is dry again. When the shot goes back to the kids after the close-up of the treasure, Mikey's hair is once again wet before he steps through the waterfall. It also happens several times in the passageway with multiple characters.
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.
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 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.
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.
While the Goonies are looking at the printouts of the counterfeit money, Stef is seen in the background trying out the telephone. She hangs it up as if it is not working. Later Chunk uses the same phone to call the sheriff.
It is not established how the doubloon ends up with Chunk so that the Fratellis are able find it (but this was probably filmed and deleted because the screenplay indicates that Chunk retrieves the doubloon when the Goonies all fall to the floor after being frightened by Sloth).
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.
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.
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.
Mikey's dad's first name is established in dialogue as "Irving." He signs "Irving" on the foreclosure paper in the final scene, but the form actually says "Michael Walsh" (typed in two different places). (And odder still is that Mikey's dad's name is Andrew in the novelization.)
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.