The pilot of the plane incorrectly says the word "five" as "fiver". In standard radio phonetics, the number "nine" is pronounced "niner", to distinguish it from "five", which is not changed or pronounced "fife".
When ending the radio conversation, policeman says, "Over and out". This combination does not exist in standard radio communication protocol where only "out" is used to end the conversation (while "over" indicates passing the voice over to the other side).
The first shot when Scout Master Wars is recording his message, you see the recorder, a glass half full, an ashtray and a picture on the table. From the opposite angle, his hand appears over the ashtray, the glass now almost empty and the picture angle and distance from the machine all change.
When Scout Master Ward asks "Who's missing?", there are nine scouts at breakfast mess and one empty chair (at around 42 mins), but there are eleven scouts in Troop 55. In addition to Sam, Lazy Eye is also missing from the mess table. He reappears (at around 15 mins) when ten scouts and Scout Master Ward peer into Sam's tent.
An overhead shot of the police station wagon driving across the island shows a smooth top and just the red light. In later shots, the station wagon has a rack on the top and a siren in front of the red light.
When Suzy goes into the tent by herself, she is wearing a heavy layer of blue eye shadow. A few moments later when Sam enters the tent, Suzy has been crying and her eyes are nearly devoid of shadow before Sam hands her his neckerchief and she wipes her eyes. In the very next scene when Suzy is reading aloud from her one of her books, her eyes are once again fully coated with eye shadow.
When Scout Master Ward first comes out of the exploding hut after rescuing Commander Pierce, Commander Pierce's hat is off. When they turn around to evacuate the area with the other scouts, Commander Pierce's hat is on to disguise it being a dummy on the Ward's back.
At the beginning of the movie, Suzy looks out through a window using binoculars. When shot from the inside she is in the top attic room looking out through a dorm window. When shot from the outside she is in the middle tower room.
When Sam is alone in the canoe, the camera shows a closeup of his patches and the brooch that belonged to his deceased mother. When the camera shows Sam's full body, his life jacket is completely covering all of those items.
When Scout Master Ward enters Sam's tent at Camp Ivanhoe, he discovers that it's empty and that Sam has left via a hole in the side of the tent. The hole is covered by a map, but it's taped to the inside of the tent. If Sam had actually left via the hole, he would have no way to stick the map to the side of the tent, and if he had left via the tent door - which was zipped with the zipper-pull on the inside - there would be no reason for the hole in the first place.
The recording which contains "The Carnival of the Animals" and the "Young Person's Guide to the Orchestra", both conducted by Leonard Bernstein, is a 12-inch LP which plays at 33 1/3 RPM, not a single that plays at 45 RPM.
The goof item below may give away important plot points.
There are numerous inconsistencies between the map shown in the beginning of the movie during the narrator's introduction of New Penzance, and the two maps shown later in the movie when Troop 55 rows across the Cold-Water Strait and when Scoutmaster Ward sends a message to Fort Lebanon. The map in the beginning of the movie shows that there are no islands in Stone Cove, but the later maps do have an island; the size, shape, and position of Belgian Hours change in the later maps compared to the first map; Lily's Look-Out, Polish Prince, Treasured Indian Grip, and St. Jack Township are labeled farther east on the first map compared to the later maps. There are also many coastline inconsistencies between the first map and the later maps.