In the scene where the submarine is using a torpedo to trigger mines, the torpedo triggers a mine but can be seen continuing on its course without damage.
When they torpedo the net tender you can see it beginning to sink before the torpedo makes contact.
The first ship they sunk is accomplished with one torpedo. American torpedoes, until well into the war, were so unreliable (50% or less due to a hidden flaw in its fuse design and manufacture) that it was typical to launch 3 or 4 torpedoes at each target to ensure that at least one would hit the target, but more importantly that one would explode upon hitting the target. Returning from patrol having fired 18 torpedoes and sinking 4 ships was not unusual.
Officers are seen wearing hats while at their duty stations on the submarine. Hats/caps are not worn indoors/inside.
At about 1:16, the captain asks the depth and is told 30 fathoms. He then orders that the boat be taken "down to 90 feet." A fathom is 6 feet, so 30 fathoms would be 180 feet.
Towards the end of the film, when the Grayfish is lying on the bottom, the captain urges the radioman to keep trying to contact the Bluefin (the other submarine) on the radio, and the radioman replies, "I'm broadcasting, sir," while he works his Morse Code key. The Bluefin eventually answers. Conventional radio signals will not penetrate underwater.
However, the QC sonar onboard WWII submarines was set up so that it could be used in conjunction with a straight key for Morse Code sonar pulses for emergency communication, so the scene depicted is plausible.
The first ship they sink is sailing backwards for no apparent reason.
In one scene which takes place at Pearl Harbor, the USS Marsh, DE-699, can be clearly seen in the background. The Marsh was commissioned in January of 1944, and could not have been at Pearl in 1942 when this movie takes place.
When all bow torpedoes are shot at the anti-submarine net from inside Tokyo Bay to blast a hole for the sub to escape, as the torpedoes are shown speeding away from the sub and toward the camera, when they get close to the camera the guide wires on which they run can be seen.