The SNARK cleans sand and rock debris from around the sunken sub's escape hatch, but when the rescue vessel arrives later, the submarine is completely clean; all the debris is gone.
The concept of using a shaped charge underwater is somewhat of a fallacy. In normal circumstances the nature of the surrounding air would allow for a great deal of compression which allows the charge to work. Even so, the explosion still has some degree of impact in all directions. Water, however, does not compress, which greatly reduces the directionality. The impact would still be enough to rupture the hull.
When resting on the bottom, the crew are seen on the mess decks watching a movie. In real life, the non-essential crew would have been sent to their bunks and the ship would have been placed on reduced electrical load in order to preserve precious battery power. There would not have been any movies or cooked meals.
A sailor on the DSRV has an American flag on his arm. It is facing the wrong direction. The blue field should always be towards the front, as if the person is facing into the wind.
The captain of the Norwegian freighter is in fact speaking Swedish with a few Norwegian words thrown in. And his crew members are speaking Norwegian with very poor Americanized pronunciation.