(at around 19 mins) In one of the scenes, the Executive Officer calls LCDR Dodge "Commander". While the "Lieutenant" modifier is often omitted from lieutenant commander (or lieutenant colonel, for that matter), this is considered insulting in context, as LCDR Dodge was the Commanding Officer (CO) of the Boat, his correct title would have been "Skipper" or "Captain".
(at around 34 mins) When Knox rejects the possibility that a Diesel-powered contact could be a submarine, he ignores the fact that the US Navy is the only navy in the world with an all-nuclear submarine fleet and frequently exercises with allied navies.
(at around 1h 19 mins) The Diesels on the Balao class boats did not connect directly, or through a transmission, to the screws. Rather, they powered generators, which charged batteries and ran the electric motors which did power the screws. Therefore, thinning the fuel-air mix, as CPO Howard does by adding whiskey in the final chase sequence, would not affect the RPMs available to the screws, even if it did slightly increase the power being generated by the engines.
For the majority of the film, Lake is seen wearing an Officer's Surface Warfare Insignia. At the end, she has an Officer's Submarine Warfare Insignia. Both of those insignia can (and should) be worn on the uniform. The one for your primary warfare area (in this case submarines) above the ribbons, and the secondary warfare area below the ribbons on the pocket flap.
(at around 1h 26 mins) At the end of the movie, Jackson is seen in formation with hair growth on his chin. Since it was shaved throughout the movie, he obviously did not have a "no shave" chit (as offered by the Navy for some medical reasons). Therefore, this growth would have been unauthorized.
(at around 36 mins) When Cmdr. Dodge sends Jackson up the periscope to mount the drop light, the roll of duct tape is in Dodge's hand when Jackson is climbing, yet in the next view Jackson has the tape.
(at around 1h 17 mins) When Cmdr. Dodge looks through the periscope before surfacing for the final attack, he says that the low clouds will hide them from aircraft. But once they surface, all the action takes place under clear blue skies.
When the Stingray is shown moving under the SS Denali the stand for the bow running lights, which should only be used when the sub is surfaced, is clearly visible. But when the Stingray surfaces for its torpedo run it shows no stand.
The sonar screen shown as the Stingray begins its torpedo run shows the same 'picture' as it does when the blockading vessels begin pinging before the Stingray hides under the Denali, even though the Dodge states that they are past all the ships and only the Orlando was near.
(at around 10 mins) Sylvesterson was the first sailor picked to board the boat, but when he walks up the plank when boarding the boat, RJ Jackson is seen walking behind Dodge, not Sylvesterson. Where did Jackson come from?
(at around 4 mins) In the opening scene when Captain Knox gets up out of his chair to congratulate Dodge on his promotion, Dodge is clearly seen folding up his orders to shake Knox's hand. As he turns to walk out of the Captain's cabin, the orders are unfolded in his hand again.
At about 1:20:06, submarine Orlando confirms torpedo range, with guidance lock on the Stingray, at a distance of approximately 4,785 yards. At approximately 4,245 yards,the Orlando acquires the shooting solution. But before the solution was acquired, 'Sonar' on the Stingray informed Dodge that the Orlando was 3,000 yards away and closing. That means Orlando would have defeated the Stingray well before the torpedoes were fired at the dummy ship.
When attacking Norfolk, Virginia, mountains can clearly be seen in the background. This region of Virginia has no visible mountains. As seen in the Filming Locations these hills are in the San Francisco Bay Area.
(at around 2 mins) The golf course at the Naval Submarine Base of Groton, CT is north, or past, the sub base when coming in from Long Island Sound. The USS Orlando would have to have gone past the base and turned around in the narrow Thames River in order for the boat to be facing south and Lt. Cmdr. to take his golf shot aft of the sail.
(at around 1h 17 mins) Near the end, when the Stingray is making the run on Norfolk, Dodge surfaces to run faster. This is correct for a diesel submarine. Admiral Graham surfaces the USS Orlando, presumably for the same reason. However, a Los Angeles class submarine, like all nuclear submarines, can actually run faster submerged. When comparing the specs, the Balao class USS Stingray's top speed would be 20.25 knots on the surface, but the Los Angeles class USS Orlando's top speed is quoted as 20 knots on the surface.
If the Orlando could close on the Stingray at all, it wouldn't be nearly as quickly as shown.
(at around 1h 24 mins) At the end of the movie the crew exit the sub through a covered hatch. This cover is only present on the USS Pampanito for the use of tourists and would not be found on an actual Navy sub.
Both the SS-number and the name are inaccurate for this design of submarine. The true SS-161 was a 4th-group 'S'-class boat (originally numbered as the 'S-50') built in 1920-21, and had been scrapped by 1932. The true 'USS Stingray' was a 'Salmon'-class submarine with the number SS-186. It was constructed in 1937-38, served and survived WWII, and was scrapped in 1946.
(at around 40 mins) When Graham informs Winslow that he is "...in line for a third star." Winslow reacts with "I'll no longer outrank you.". Even though they would be the exact same rank Winslow would still outrank Graham since he has more time in grade. Something a senior admiral should know.
(at around 1h 10 mins) The MV Denali, the tanker the Stingray uses to sneak into Norfolk toward the end of the film, only has one propeller. The underwater shots of the Stingray's approach show it with two.
(at around 2 mins) At the start of the film we see Cmdr Dodge playing his golf shot at the rear of the submarine's sail when the Orlando's Skipper calls down from the top of it. This is not possible because the only area where a person can stand when at the top of the sail is on the bridge, which is a further 20 feet forward at the front of the sail. There is no possible way to move from the front to the back without walking on top of it.
When the 'Stingray' passes between the two propellers of the tanker in its attempt to sneak into Norfolk, the propellers are shown to be at a level approximately half-way down the hull of the 'Stingray'. However, the 'Stingray' was said to be a WWII-vintage 'Balao'-class submarine and the distance from bottom of keel to top of the conning tower was something like 60 feet. This would mean that the propellers were suspended at least thirty feet below the hull of the tanker, which is completely contrary to modern ship design.
(at around 1h 7 mins) When Dodge asks for the surface picture prior to hiding beneath the Denali, Sonar says there are 5 Destroyers, 3 Frigates and the Denali. After that point, in the shots of the surface ships conducting the search for Stingray, all of the ships are Ticonderoga class Cruisers.
(at around 27 mins) Dodge orders the sub to a depth of 500 feet. The test depth of a Balao-class submarine is 400 feet. No captain would ever exceed the test depth for anything other than a last resort. To do so would subject the captain to a court marshal.
(at around 1h 4 mins) RAdm. Yancy Graham says, "He's gone AWOL with U.S. government property". AWOL, Absent With Out Leave is Army terminology. The Naval term is UA, which is Unauthorized Absence. However the producers felt the audience would recognize the meaning of "AWOL" but not "UA".
When they first learn of the approach of the nuclear sub, Dodge orders the diesel engines shut off and then orders them to surface. Diesel subs run on battery power while submerged. There is not enough air to run a diesel engine underwater.
Lt. Cmdr. Dodge has had a bizarre career, as rank is concerned, in the Navy. He is clearly a mustang (noncommissioned officer who, after an OCS course, receives a commission), as after 20 years (according to his conversation with Cmdr. Knox) he is only a Lieutenant Commander (equivalent to a Major in ground/air forces). Despite this, he appears to be approximately the same age as Cmdr. Knox - who perhaps is another mustang. On top of that, "the Murmansk brushing incident" is stated to be both three years ago and while he was an ensign. It is also mentioned as an (understandable) obstacle to promotion, but Dodge has been promoted three grades in as many years since - clearly somewhat faster than the average officer should expect promotion.
(at around 26 mins) During the initial dive of the SS-161 Stingray, the sub is tilted due to an air pocket. When viewing cast during this scene, some are angled the same as the ship, indication that the only thing tilted was the camera.