(at around 1h 22 mins) When the crew comes out of the sub from the forward torpedo room, they walk up stairs. In submarines during the war, there were no stairs out of a ship; sailors climbed up ladders through hatches. They walked through the forward torpedo loading hatch that was opened, and stairs were added to the sub after turning it into a museum ship to make it convenient for tourists to enter and exit the sub.
(at around 4 mins) The diving officer orders the boat to periscope depth, then adds, "65 feet." On a WW2 fleet boat, the minimum periscope depth was 55 feet, the optimum was 58 feet, and the maximum was 62 feet. At 65 feet, the scope would have been three feet under the surface.
(at around 1h 35 mins) The British ship wouldn't have flown the Union Flag (often called the Union Jack) at the stern as this is never used as an ensign (the flag at the back of the ship). The ship shown in the movie (the fictional RMS Archimedes) is a merchant ship so it would have flown the Red Ensign, which is red with a small Union Flag in the top corner nearest the flagpole.
(at around 39 mins) The use of grappling hooks was not an anti-submarine tactic used by the German Kriegsmarine during World War II. That tactic was used by German and British naval forces during World War I, but only in shallow water. There are also reports of the Japanese Imperial Navy using hooks in the Pacific during World War II.
Even in peacetime, submarines never went to sea with their safety lines and stanchions rigged.