Revealing mistake: When the men are waiting at the dock and when boarding the submarine, we see the wide shot of the submarine and the dock. The ocean is, however, incredibly calm despite there being torrential rain happening throughout the scene on the dock. While it's not seen, this would be from a rain machine not able to cover the entire location of the shot. (00:13:51 - 00:16:38)
Revealing mistake: After the XO orders all stop, we see a close-up of the ship's yoke being pulled back. The next wide shot shows the interior as the bow of the sub is rising, and just before this shot ends, note the console that the man with headphones is working at. A pair of crewmembers cross paths in the foreground, then the entire console wobbles, proving it isn't attached to the floor at all. (01:09:00)
Answer: In the most technical sense ("by the book") it is against policy. But then, the Marines do not allow tattoos and look how well that's enforced. It is up to the ship's Captain to enforce such regulations, and at sea, there's no one to penalize him if he chooses to let the crew smoke at certain times, given certain conditions.
johnrosa