Revealing mistake: At the start, when Data is being pulled towards the chained orange drum, due to the angle of the close-up, we see that the soles of Data's Nikes are not actually touching the ground (since there is a rolling mechanism under his feet). Despite the fact that Data is quite inventive, we see in the next shot there's nothing attached to Data's Nikes. (00:03:55)
Revealing mistake: During the police chase, when the Fratellis turn left in the close-up (just before the shot of Mouth's TV), sitting in the passenger seat instead of Francis we see a man who is taller, wears no glasses and is at least 25 years older than our Francis. Also note the man who is driving instead of the real beloved Mama Fratelli. (00:03:10)
Revealing mistake: Up in the attic, when Chunk walks over to Mikey (who wants Chunk to drop the frame), at that moment Data and Brand are alone, and while the two of them are looking at the plasma lamp Brand flicks the glass with his finger, and just as Data stares at Brand we can clearly hear Data say, "Don't touch it Josh!", which is Brand's real name. (Mikey does the same thing later at the lighthouse restaurant.)
Revealing mistake: When the Fratellis get a visit from the bats out of the basement, two bats fly in front of Jake Fratelli and while they are flying in front of him you can clearly see their wires.
Revealing mistake: At the Astoria Country Club, when Troy first sits down in the stall and opens the magazine, behind him are at least nine columns of small patterned tiles. In his next close-up as he looks around, the wall behind him is completely different. Now there are only six columns of larger unpatterned tiles, with a long vertical gap between the tiles (where the grout should be) - which is the track for the mechanism to lift Troy in the following shots. (00:51:00)
Revealing mistake: Just as Mikey opens the front door for Data's entrance, the porch upper rail is seen right outside the doorway, with the chimes hanging from it. The problem here is the long wood plank at the top corner of the porch railing, that has been added to the decorative bracket that's seen in all other shots. (00:08:55)
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)
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)
Revealing mistake: When all of the Goonie kids run upstairs to the attic, they rush past the camera, and you can see the image wobble slightly, as if one of them jostled the cameraman.