The length of Jonesy's facial hair changes throughout the movie.
When Beaver drops the toothpicks in the bathroom, he still has one in his hand. In the next shot, the toothpick is gone.
When Lt. Underhill is in the car, he loads a cartridge into his pistol by pulling back the slide and releasing it. The pistol is a Model 1911, which loads a cartridge and cocks the hammer when you pull back the slide. Lt. Underhill immediately sets the pistol down in the center console, but the hammer is now down, no longer cocked.
When Beaver and Jonesy are following the trail of blood, Beaver's shirt is alternately wet and dry between shots.
When Henry shoots his diploma, the bullet goes through the glass and the diploma immediately below the word "University". In a close-up of the diploma, the bullet hole is at least an inch below Henry's name.
The call of a loon can be heard in outdoor scenes. The film is set in winter, when loons would've migrated south for the winter.
When Jonesy and Beaver return inside the cabin after seeing the helicopters, Jonesy is wearing blue sneakers. When they notice the trail of blood and Jonesy steps over a puddle, Jonesy wears black boots.
When asked to swear he was telling the truth, the young serviceman gave the Boy Scout "sign" not any salute. Col Curtis (Morgan Freeman) as him to describe Blue Unit, the unit to which the serviceman belongs. He says they operate under the radar, they are not regular army, they do not salute, they do not display rank. When Col Curtis asks him about the incident, he asks the serviceman "Scout honor. Can you raise your hand tell me honestly you know this for a fact?"
When the lighter fluid on the floor is ignited, the heads on the matches lying in it don't ignite, revealing that they aren't real matches.
When Col. Curtis in firing the mini-gun at Lt. Underhill from the helicopter, the sound it emits is a conventional machine gun, not the unique whir of a mini-gun.
When Beaver fights the weasel in the bathroom, a cable for operating the puppet is visible, attached to his shirt. It's most visible in a close-up of his chest as the weasel lunges at him.
As Henry leaves the general store just before the snowstorm, a crew member standing on a ladder is reflected in the driver's side window of Henry's truck.
When Beaver sits down at the table with the peanut butter you see a camera moving on a line in the background as he says: I saw that once in a movie".
When the pistol's tracking device is monitored, the marker shows Interstate 95 running west of Dixfield, Maine. The closest I-95 gets to Dixfield is Auburn (Exit 75, about 35 miles southeast) and Augusta (Exits 104, 112, and 113, almost 50 miles east).
LTG Matheson's rank insignia on his beret is clearly upside-down.