Toward the end of the film, after Duke kisses Mary Stuart, she holds his right arm to follow him. In the next shot she is turning around the left arm to hold his arm.
While Duke is in the admirals office trying to convince the admiral to allow him to stay aboard the thunder over John Wayne's shoulder is a calendar with the distinctive outline of a C-97 a cargo variant of the B-29. This aircraft didn't see service until 2 years after the end of the war.
At about 1:05 into the movie, when the Brass comes back topside after meeting with the crew John Wayne's Character is seen wearing a very short, very wide tie, as the Brass leave it cuts to him wearing a longer, thinner, more uniform tie.
Duke walks in the hospital corridor holding the cap in his right hand. In the subsequent shot he appears in front of the nursery, holding the cap with both hands.
When Pop gives the order "Cast off for'ard", the person behind him is holding a microphone below his chin with his left hand. In the subsequent shot his left hand holds the left earphone.
Mary Stuart was allowed into the ComSubPac plotting room. It is next to impossible to believe that a highly secret room like that (with location and position of the entire Pacific Fleet) would be accessible to common US Navy Personnel like nurses.
The studio set is much larger than a wartime submarine would have been.
The submarine officers were wearing silver Dolphin pins. Officers wear gold Dolphins.
It is impossible for a sailor to communicate with an airplane by using a sound-powered phone.
The pictures of a large splash immediately after the Thunderfish fires torpedoes are incorrect. These are torpedoes launched by a surface ship. A submarine launched torpedo should never break the surface.
One of the torpedoes fired from the sub is pulled by a visible cable.
During the depth charge attack the sub is supposed to be at a depth of 120 feet yet she is near the sea floor and the surface is obviously only a few feet above her. The area where the action is taking place has a depth of well over 1000 feet. At 120 feet she would be nowhere near the sea floor.
When the dummy torpedo warhead is being hauled up by crane and dropped on a target to test the new firing mechanisms, 3 tests are performed. All 3 tests are the exact same piece of footage. You can tell by the way the warhead bounces when it hits its target, the same 2 seamen are to either side of it in the foreground in all 3 tests, and the left seaman jerks his right arm to the left in exactly the same manner in all 3 tests.
When the Thunder is "depth-charged" near the beginning of the film, it's US Navy sailors who are dropping the cans. Only a few frames are shown, but it's clearly US Naval personnel (possibly stock footage).
The first ship sunk on the second patrol has US Navy numbering on its bow.
As the sub is attempting to dive after discovering that the ship they had attacked was a Q-ship. The Captain and the inside of the conning tower is hit by bullets, not bullets that had penetrated the steel that made up the metal of the conning tower. Those bullets would have had to come from behind and above. And the Q-ship was not high enough to fire down on them and hit them behind the nearly chest-high bridge enclosure. The gun would have had to have come from behind, and the Q-ship was in front of them. Also after the captain was hit, a crewman came back up out of the conning tower hatch to attempt to pull the captain below. He too was hit by machine gun fire. Something that would have been impossible by anything but an attacking airplane.
In the opening scenes the stenciling on the life rafts show the date of manufacture as 8/49 which is approximately four years after the end of the war.
The final attack on the carrier left behind by the Imperial fleet makes no sense. Carriers were the most important vessels in a fleet, and would not be left behind without an escort of more than a single destroyer, especially in the presence of an enemy submarine. If the carrier had been too badly damaged to be saved, it would have been destroyed by its own fleet.
At the Pearl Harbor brig, the Shore Patrol commander complains that the crews of numerous submarines are brawling with his men, naming the Tang and Wahoo among them. These two boats could not have been operating from Pearl at the same time, as the Wahoo was lost in action in October 1943 and the Tang did not enter the war zone until the following January.
The fight with the "decoy vessel" was a complete plot fabrication. The Imperial Japanese Navy is not known to have operated specific submarine decoy vessels (commonly called Q-Ships). These were used by the Allied Powers, primarily by the British Royal Navy and the United States Navy as well as the German Navy in the Atlantic. Had this been an actual depiction of a fight between a Q-Ship and a submarine, the submarine would not have surfaced, as that is exactly what a Q-Ship would have wanted. Also, even rammed, a decoy ship would be extremely hard to sink, as they were usually filled with extra flotation (typically wood) to keep them afloat after taking damage.
In the attack on "the whole Imperial fleet", the vessel actually shown to be hit is a merchant ship, something which would not be present in a group of warships.
When the Thunderfish dives under to come up astern of the Japanese decoy ship, it's clear both ships are in a diving tank.
When the lookout spots the oil slick and debris field, the boom mic shadow is visible on the sailor standing on the port side of the bridge (opposite Gifford).