The last animation of the whale shown in the film also shows about three seconds of Captain Ahab tied to a rope on the whale. He seems to have both of his legs again.
The Seaman is counting down the distance to Moby Dick and says, "2,000 yards." A glimpse of the sonar is then seen which shows the distance is between 900 and 1,000 feet. This is about a 5,000 feet or so difference.
Captain Ahab badly slashes his hand on the harpoon point enough to drip a lot of his blood over it, but then manages to steer a zodiac with it without bandaging it. Then, on the island, he shows the palm of his hand and there is no sign of the cut.
On the island after Captain Ahab puts on the wooden cross to replace his left leg, they walk to the shore. While he is standing and talking to the crew, his left leg is clearly visible. When he starts walking again, the wooden cross is back.
None of the uniforms and insignia (or lack thereof) are appropriate for U.S. Navy personnel in the situations shown in the film.
The U.S. Navy does not currently, nor has it ever had, a provision for either Enlisted or Officers to continue serving in Active Duty Status after losing a limb. Captain Ahab's loss of a leg as a Seaman would have meant he would have been given a medical discharge after the limb's loss. He would not have had the chance to be discharged as an Enlisted and to rejoin as an Officer.
The SubRoc was launched from a torpedo tube, not a vertical launcher as shown in the film.
The U.S. Navy discontinued using the SubRoc weapon system in 1989, long before the film takes place.
The interior scenes of the USE Pequod in the film in no way resemble the interior spaces of an actual U.S. Navy attack submarine. The most blatant errors are the large open spaces and the lack of electronics equipment.
In the film's opening scene, the Captain of the submarine tells his crew that they are about to enter Soviet waters, but the location information on the screen just before he says this states that they are already 50 miles inside Soviet waters.
Dr. Michelle Herman removes her headphones three times in her opening scene in the dingy, depending on the camera angle.
The skyline (Long Beach?) behind the San Diego and Point Mugu scenes is identical, yet the two California locations are nearly 200 miles apart.
Even the most powerful machine guns or machine cannons cannot fire projectiles which will penetrate water for more than a few feet. For the USE Pequod's hull to have been hit by such bullets, the boat would have had to be at a depth which would have the submarine's sail out of the water.
No U.S. Navy ship commander whatsoever has the authority to use a nuclear weapon without permission from the command authority of the United States. This restriction is deeply ingrained in the U.S. military and would, without question, result in the Officers of the ship turning on the Captain at any attempt to use such a weapon on his own authority.
It is suggested that the USE Pequod should have shot down the Osprey with a Tomahawk, not a SubRoc. Neither the Tomahawk (a cruise missile) nor the SubRoc (an antisubmarine rocket/torpedo) is capable of engaging aircraft, as any U.S. Navy Officer would know.
It is stated in the film that Captain Ahab performed modifications on his submarine. Changes to ships of the U.S. Navy require extensive documentation and approval by the Naval Sea Systems Command (NAVSEA). No individual ship's Captain has the authority to make the changes that are described in the film.
The commander of a U.S. Navy ship does not have the authority to suspend the rule of habeas corpus (the "Suspension Clause" of the U.S. Constitution). To take the action shown without orders from a higher authority would be a severe violation of the Uniform Code of Military Justice (UCMJ). The Executive Officer of the submarine would have been well aware of this.
Captain Ahab justifies his abandoning of the cruise ship survivors by describing the mayhem which Moby Dick would cause in Pearl Harbor. Pearl Harbor has a depth of, at the most, 45 feet. There is simply not enough water for Moby Dick to enter the harbor. Any Pacific Fleet ship commander would be well aware of this, since the relatively shallow depth of the harbor limits the speed of any ship therein.