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.
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.
There was no such ship as the Shinaru leading the Japanese attack on Pearl Harbor. There were six aircraft carriers, all of them committed planes to the attack. Akagi, Kaga, Hiryu, Soryu, Shokaku and Zuikaku. The first four listed were all sunk at the Battle of Midway in June of 1942. The others were sunk later. Shokaku was sunk by the submarine USS Cavalla in June 1944, while Zuikaku was sunk by aircraft in October 1944 during the Battle of Leyte Gulf.