Revealing mistake: When all the kids are in the diner just before Chunk knocks over the water jug, Mikey starts to bang on the ground with a bar. When Brand stops him, Mikey calls him by his real name Josh. This is verified on the DVD by Sean Astin himself, in the commentary.
Continuity mistake: After Chunk does the 'Truffle Shuffle' and Mikey releases the bowling ball, we see the horizontal piece of wood that is painted red and attached to the porch rail, from which the silver bucket is lowered. It's seen in many shots. What's funny is that in the first shot of the Walsh's house, after the Fratellis drive past at the bottom of the hill, that piece of wood is white, because it hasn't been painted red yet by the crew.
Continuity mistake: On the beach, when Mr. Walsh is tearing up the contract we see the bits of torn paper, but when he tosses them in the air there are many more pieces of torn paper up there.
Audio problem: When Chunk flags down the car for help, he finds Jake Fratelli, who begins to sing loudly in Italian. Chunk screams, and as we hear Jake continue singing, we see his reflection in the side-view mirror as he is smoking a cigarette silently.
Other mistake: In the final scene where they are being asked what was the scariest part of the trip, Data replies "the octopus" when the scene containing the octopus was deleted. The scene is shown on the DVD's Deleted Scenes.
Other mistake: When Troy is in the country club restroom and is sitting on the toilet, he has his trousers down around his ankles. When he gets shot up and crashes into the ceiling, you will notice he has red briefs on, but surely he would have pulled them down too...
Other mistake: With Andy weighing at least 100 lbs, surely Troy and the guys trying to pull "her" up would notice that a bucket carrying the sweater is nowhere near the weight of a person. Even if they filled it with coins from the wishing well, it still wouldn't come close to the weight of an actual person, regardless of how idiotic and pompous Troy is.
Continuity mistake: When Brand hangs upside down from the bar, we can see that the kitchen table and four chairs are right in front of the kitchen window. But when Mikey unrolls the map in the kitchen, Chunk, Data, Mikey and Mouth are standing directly in front of that kitchen window, which is completely impossible to do.
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.)
Other mistake: When Andy plays the bone organ, the musical score on the back of the map clearly shows a melody consisting of single notes with only one or two chords. Still, Andy presses multiple keys on the organ to create chords EVERY time, not some single notes as the code shows. The code should not have worked if a person was playing only chords.
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.
Continuity mistake: In the beginning, when the Fratellis are eluding the Police, Chunk witnesses the chase. In the first shot the slice of pizza is on the window. Next shot Chunk holds it in the air, and in the third shot the pizza is back in its place where it was in the first shot, with a saucy smear on the window.