There has been another collision between a nuclear submarine and another vessel. This one took place during July 2016 near Gibraltar. A British Astute class SSN (nuclear attack sub), HMS Ambush, came too close to a civilian freighter and suffered superficial damage to the “sail” (the large structure on top of the sub). There was no visible damage to the commercial ship, which continued moving because it did not notice the collision with the submerged (just beneath the surface) sub.
These collisions are rare and with the most recent one that makes three such collisions since 2009. There may have been others as some nations try to keep these incidents secret. Western navies are the most forthcoming. In January 2013 the USS Jacksonville (a 7,000 ton Los Angeles class boat) had part of a periscope sheared off by a passing fishing boat. The sub noticed that part of one periscope was gone. Apparently the fishing ship did not notice the 5 AM incident at all and no ships reported any damage later. The Straits of Hormuz are a crowded waterway often used by American subs but these underwater collisions take place elsewhere as well.
In October 2015 another SSN, the USS Montpelier (a Los Angeles class boat), collided with an American cruiser during training exercises off Georgia. The accident occurred when the sub began surfacing 200 meters in front of an approaching cruiser. Someone on the bridge of the cruiser noted this and ordered the engines to reverse but there was still a collision. The sonar dome of the cruiser was damaged as was the rudder on the sub. Nothing serious but still embarrassing.
Surfacing subs are supposed to use their passive sonar to detect the engines of any nearby ships, at least until the boat is about 15 meters (46 feet) from the surface, at which point the periscope can be used to look around at who is coming from where. That is often not sufficient to prevent a collision. To deal with that the U.S. Navy developed small buoys that can be sent to the surface via a cable (containing a power and fiber optic link with the sub). These buoys can be expendable (used once) or retrievable. Another system in development uses a light sensor on the top of the sub that can, during daylight, capture images of what's on the surface while the sub is at a depth of 60 meters (183 feet).
Sometimes the damage from these collisions is pretty bad. In early 2009, the submarine USS Hartford managed to collide with an American amphibious ship. As a result the captain and chief of the boat (senior NCO) were dismissed shortly after the March 20, collision. The 24,000 ton amphibious ship (the USS New Orleans, LPD 18) collided with the submerged Hartford (a Los Angeles class boat) in the narrow Straits of Hormuz. Fifteen sailors aboard the sub were injured, while a fuel tank on the LPD was torn open and 100,000 liters (25,000 gallons) of fuel oil got into the water. The Hartford rolled 85 degrees right after the collision and substantial damage was done to the sail, including a leak. The Hartford went to a Persian Gulf shipyard for emergency repairs (a metal brace for the sail, which was twisted so that it leaned to the right). Temporary decking, railing, and antennas were added to the topside of the sub, to make it easier for the surface ride home. Nuclear subs rarely spend this much time on the surface. The accident happened at 1 AM local time.
Initially, the accident was blamed on sloppy leadership by the captain and the senior chief petty officer. The subsequent investigation found that lax discipline was tolerated throughout the ship. This led to sloppiness. In particular, the crew did not take all the precautions mandated for passing through a narrow waterway like the Straits of Hormuz. The investigation found many specific errors the crew made that contributed to the collision. This included supervisors not staying with the sonar operator, who, it turned out, was chatting with someone when the collision (that the sonar would have provided warning about) occurred. The navigator was doing something else, while listening to his iPod, while the officer in charge did not do what he was supposed to do, check the surface with the periscope. The list went on and ultimately amounted to 30 errors in procedure.
It was an expensive accident, which cost the U.S. Navy over $100 million for repairs. This included a hull patch, plus extensive repairs to the sail (that structure on top of the hull) and one of the retractable bow planes (a wing like device). The damage to the amphibious ship (the USS New Orleans) was minor and repairs cost $2.3 million. The Hartford arrived back in Groton, Connecticut from the Persian Gulf on May 21st. The Hartford took over a month to make the trip because it had to do it all on the surface (SSNs move faster underwater than on the surface). This was because of the damage to the subs sail.
The Hartford repairs were more than what it cost to replace the front end of the SSN USS San Francisco, which ran into a sea mount in 2005, and stove in its sonar space (the front of the boat). A front end from a retiring SSN was taken and fitted on the San Francisco, costing about $80 million.
This is not the first time the Hartford has had an underwater misadventure. In 2007 the Hartford grounded itself while training off the Spanish coast. It was only after the sub was dry docked that it was discovered how serious the damage was. The bottom half of the rudder was torn off and the gouges in the hull were deeper than first thought. Although the sub was able to steam back to dry dock facilities at Groton, Connecticut, it had to do so at half speed, taking a month for a trip that normally is made in two weeks. The cause of that accident was sloppiness by the six sailors in the navigation team. Too much time was allowed to elapse between position updates and the sub went aground while navigating shallow coastal waters. All six sailors in the "navigation party" were punished for dereliction of duty. The captain of the sub and his boss (the commander of Submarine Squadron 22, based in Spain) were both relieved of duty. The implication here is that the training and discipline of the navigation party were not up to standard and the ship's captain and the squadron commander are responsible for training and discipline. The damage to the Hartford required expensive repairs to the hull and kept the sub out of service for nearly a year. The same thing is happening again.
All these accidents are part of a larger problem in the navy, finding and retaining sailors capable of running a nuclear submarine. Sub commanders are under a lot of pressure to keep their sailors from leaving the navy. But the long periods submarine sailors spend away from their families creates pressure to get out and take a civilian job close to home. The submarine sailors are very capable, and highly trained, people. Getting a better paying civilian job is not a problem. So sub captains try to keep the crews happy. That often leads to lax discipline. And that often leads to these collisions. Many sub captains see this as a calculated risk, as they know that, in wartime, their highly skilled crews would snap together and do the job. But a sub commander’s first priority, at least in peacetime, is the safety of his boat. In wartime the mission comes first.
There's precedent for this. During the early days of World War II, the U.S. Navy had to replace most of its sub captains. These men had risen to their positions in the peacetime navy by doing things by the book and always adhering to procedure. But in combat you needed much more flexible commanders, and these were the ones who came in and won the American submarine war in the Pacific.