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.
Other mistake: After the kids find Chester Copperpot's skeleton, Mikey picks up Copperpot's book and finds the Gehrig baseball card inside. When Mikey turns the card over it's the 1973 Topps Lou Gehrig All-Time Grand Slam Leader #472 (which has nine players' grand slam stats listed on the back of the card, that includes Hank Aaron who started playing MLB in 1954). The problem is Copperpot was reported as missing in 1935, but this specific Topps baseball card (now well known) was issued in 1973, nearly 40 years after Copperpot's death via the pirate booby trap. (00:54:30)
Visible crew/equipment: In the shot of Mama Fratelli waiting outside for Jake in the ORV, you can see the reflection of some film equipment in the small triangle window next to her. (00:01:30)
Continuity mistake: In the beginning scene of the cop calling out the inmates for their lunch, just as he calls "Hey Turkey." you can see the shadow of the supposedly hanged Jake Fratelli on the right wall. The shadow is totally inconsistent with the design of the cell and position Jake was hanging in. (00:00:45)
Continuity mistake: In the scene where the kids are crossing the wooden bridge near the waterfall, Data is seen holding a lantern. After he does his "slick shoes" routine, the lantern has disappeared.
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. (01:32:40)
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. (00:02:25)