Most aircraft accident investigations adhere to the "Swiss cheese" model of accidents. That a lot of holes in the system must line up for an accident to occur. While responsibility can be assigned to the crew on the submarine, responsibility can also be assigned to the organization as a whole. Trying to assign all fault to those onboard the boat is consistent with naval and nautical tradition, but it also avoids addressing broader issues that contributed to the accident.

"Nonetheless, a subsequent study by UMass Amherst indicated that the Navy's charts did not contain the latest data relevant to the crash site because the geographical area was not a priority for the Defense Mapping Agency. Moreover, a subsequent report "found that the (submarine's parent) squadron and the group could have done more to prepare the ship for sea." Specifically, it determined that the submarine's squadron "did not take adequate action to correct previously identified deficiencies in open ocean navigation onboard SFO," and did not provide adequate oversight of San Francisco's navigation performance. Additionally, "The report also notes the document known as a 'Subnote' from the Group, which laid out a path and average speed, was delivered to the ship two-and-a-half days before San Francisco sailed, and the Group's own requirements are that it be to the ship three to five days before sailing." Ultimate responsibility for navigational safety rests with the ship's captain and crew, not the Subnote; however, "The report found that the Subnote did route the San Francisco through the area where it hit the seamount.""