When Miyagi gives Daniel his last will and testament, the candles of the family shrine are not lit. In the next shot, as Miyagi turns to enter the shrine, the candles are lit.
After Daniel races Kumiko to the castle ruins, he points at her with his right hand to tell her that she cheated. In the very next shot, he is pointing at her with his left hand.
After they left the air base, it was daytime. They drove over a small bridge, and in the next shot, they were on the other side of the same bridge but it was then much darker out as if they had been driving for a while.
When Daniel and Kumiko are in the hut having the tea ceremony, we see Kumiko unclip her barrette and her hair falls and is blown about by the heavy winds. In the next shot, as she goes to kiss Daniel, both her and Daniel's hair and clothing are motionless.
At the cannery, Mr. Miyagi releases a hook from the tower and dodges it, and the sharp point slams into the wood behind him. Daniel asks him if he can try, and Mr. Miyagi climbs to the tower to reset the hook. However, when he is raising the hook, there is a large piece of wood covering the hook (as a safety). When the hook gets to the top, the hook is bare, and Mr. Miyagi places the same wood on the hook.
During the bar scene, Daniel claims that a man is "standing wrong" to perform an ice breaking technique, so he could only break through 2 pieces. The man then challenges Daniel to do better -- break at least 3 pieces. When Chozen offers 3:1 odds against Daniel breaking the ice, several patrons excitedly place a bet in favor of Daniel. Then, the man seeks to clarify the bet asking "Hey, he's gotta break all 3 right?" Chozen responds "Wrong, all 6." Afterwards, the crowd gets more excited and places more bets. This does not make sense. Any bets already made became worse upon knowledge that Daniel had to break all 6 pieces to win instead of 3. If anything, the crowd should have been withdrawing their bets instead of excitedly making more bets.
In the beginning of the movie John Kreese goes to punch Mr Miyagi in the face however, he breaks the car window instead. The car window is much lower than Mr Miyagi's face. Kreese would have had to be aiming at Mr Miyagi's stomach.
When Daniel accidentally knocks over Chozen's scale, one of the weights breaks, revealing it is fake and prompting the farmers to yell, "So you cheat people!" This would mean a cheat in the farmers' favor. However, Sato owns the land and may charge a fee to the farmers for how much they produce. If it appeared they produced more than they actually did, the fee to Sato would be greater.
When Mr. Miyagi is boarding the plane to Okinawa, the air hostess tells him that he's on seat 32 B, but when he turns to speak with Daniel, his boarding card says 32 A as his seat.
After Miyagi fights Chozen and his friends, he runs by a concrete statue to see if Daniel is okay. The statue moves a bit. The next scene shows Chozen kicking this statue and supposedly breaking it.
Just after Mr. Miyagi teaches Daniel the drum technique on the fishing dock, Daniel foolishly releases one of the hooks without the protective cork on it and it rips a circular hole in his button-down shirt. In actuality, this would be impossible since the hook is not a projectile, but rather swung on ropes. Instead, the hook would have either caught in Daniel's shirt and yanked him off the dock or ripped clean through it.
At the cannery, Mr. Miyagi releases a hook from the tower (while standing on a mount at the equilibrium of the hooks travel), dodges it, and the hook slams into the wood behind him.
Daniel asks him if he can try and climbs onto the mount.
Mr Miyagi reels in the hook but for this to happen the hook would have been pulled out of its resting place, which would result in it swinging back through the equilibrium, hitting Daniel from behind as he had his back to it.
Kumiko seems surprised about Daniel telling her that cars in the United States driving on the right side of the road. However, extrapolating that Kumiko is 18 years old, she would have been born between 1966-1968, during the US occupation of Okinawa, when cars drove on the right side of the road, and even when the US handed Okinawa back to Japan in 1972, Okinawa drove on the right side of the road until 1978. She would have clearly remembered when Okinawa drove on the right side of the road.
The village of Miyagi had been transformed into a busy metropolitan area long before the time in which the film was set. The story could have also taken place in nearby Miyagi Island which more closely resembles the cinematic version of the village, but it's equally anachronistic. Essentially, at the time the film is set, Okinawa looks nothing like the version depicted in the film; its a busy, bustling, first-world city not a rural region.
When Miyagi and Daniel are in the bar betting on the ice slabs, Miyagi says, "Miyagi take care of everything." In the next shot, he says "What odds?", but his mouth never moves.
Kadena Airbase (where Tomi Village is next to) is North of Naha, not South as Mr. Miyagi keeps insisting.
Tomi Village is located in a mountainous area, but is said to be to the south of Okinawa. Okinawa's mountainous region is to the north.
The situation where a typhoon suddenly appears near the end is unbelievable. Even in the 1980s, weather satellites would have detected and warned the population of Okinawa of the approaching storm days in advance, especially since the island is home to such an important US military base.
When the young Air Force man is giving Mr Miyagi and Daniel
directions to his village in Okinawa, he asks the "Sarge" where it is. The sergeant then replies, "You are standing on it corporal." There are no corporals in the Air Force, and his rank was actually an Airman First Class (E-3) with two stripes. The correct response from the sergeant should have been, "You are standing on it airman."
When Daniel helps the villager with the wheelbarrow to the produce scales, he accidentally reveals that Chozen is cheating people with fake weights when he breaks one. However, it's fake in that it appears to be made of foam, this would make them light, making Chozen have to use more weights, making the produce appear heavier and thus more valuable. Chozen's scam would lead to overpaying the villagers, not under as is portrayed.
When Mr. Miyagi goes to put his glasses on when he receives the letter at the beginning of the film, he sticks one of the arms of his glasses in his eye by accident before putting them on properly.