On the submarine, the captain (Richard Widmark) has a cup of coffee in his hand as the sub hits the sea bottom with a thud. Denise (Bella Darvi) who is sitting on a stool is about to fall off. The captain grabs her using both hands, the cup of coffee having disappeared.
When the landing party is making its escape from the second island, Captain Jones' hat falls off as they are getting in the dinghy. The actor is clearly a dark-haired double for Richard Widmark.
The deck gun on the submarine differs in the close-up view versus the distant view.
At 49:15 a torpedo is fired at a submerged sub from a submerged sub. A capability not available at that time, certainly not to a Chinese owned war-surplus submarine.
A WWII era Japanese submarine, I-203, did indeed exist. But I-203 was sunk by the U.S. Navy in 1946. This story takes place in 1953.
In the beginning, when the captain is introduced to his sub for the first time and at other times, a brass bell can clearly be seen outside the conning tower. No sub crew in the world would even dare to consider this - after all, you want to reduce noise.
Given that Jones is the only officer on the submarine, he would not go ashore and risk being killed or captured as it would leave the submarine leaderless.