Continuity mistake: In the scene where they are playing the bone-organ to escape, the Fratellis walk across the beam then climb the rocks to get to the room where the Goonies are. In one of the rocks there is a tall metal post sticking up. A shot shows one Fratelli brother stick his hand on this post to pull himself up, but in the next shot the hand is gone and a moment later the Fratellis emerge from the water.
Continuity mistake: When you first see Andy's hands being tied, you can see that they are tied fairly tight. Right before she goes off the plank, you'll see that the rope is barely around one wrist. In the next shot as she is going into the water, you can see her holding her elbows with both her hands. Then when Brand rescues her the rope is secure again.
Continuity mistake: When the Fratellis leave the County Jail, the first police cruiser which makes the U-turn has a smooth chrome bumper with only a recessed license plate at the center, but when they make the first left turn, that squad car now has a chrome bumper with driving lights at each end and bumper guards on both sides of the license plate. It's funny how when they make the next right turn, the car style actually changes mid-turn, between shots - just before the second police cruiser joins the pursuit.
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.
Continuity mistake: When the back of the Fratelli's ORV is riddled with bullet holes, you can see they make a distinctive backwards "L" shape above the Jeep letters. Later, when Chunk examines the ORV, the bullets holes are now in different places than they were before. Also, the license plate that is seen on the ORV when it is hit by the bullets, changes design as well.
Continuity mistake: When Data activates his 'slick shoes' on the log bridge, the heels of the shoes pop open to reveal the 'slick shoes' mechanism which starts spraying oil. In the next shot though, they show Data walking across the log, the heels of the shoes are closed, and the oil squirts out of holes in the back of the heels apparently.
Audio problem: When they are standing in Mikey's kitchen looking at the map, all you can see is their eyes above the top of the map. Right before it cuts away to the Cyndi Lauper video, the map moves down just enough to see Chunk saying something, but there is no accompanying audio.
Continuity mistake: Right after Troy is humiliated at the wishing well, the movie cuts to a television food program, with Sloth's reflection visible in it. The problem is that Sloth's face is noticeably different in this reflection than the rest of the film. For instance, his left eye is only a bit lower than his right eye now, instead of it being considerably lower like it usually is.