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I'm not a sailor or seaman, but perhaps knowing more about the officers and crew might help in understanding how they could have ignored such danger signs.

Incompetence, since they did everything wrong...
But why? Why would they not be qualified to command and to monitor and to steer and make course and speed adjustments in dangerous waters?
Why would they not be able to recognize dangerous waters?
Why would the command not respond to a seaman's concern, if expressed?
Why couldn't the seaman discern the differences?

There seems to be lots of unanswered questions. Do the answers go to the Admiralty, by chance?

A fast attack submarine is a pressure cooker. You are always 20 projects behind and it never stops.

The best submarines spend the most time out at sea. The longer you spend out at sea the more things you need to fix when you pull in. So when you pull in you get less time at the house and more time on the boat fixing stuff. It it a self escalating problem. Missile submarines have two crews to prevent this exact situation.

You get updates to maps, tech manuals and such by the truckload and there is always some poor slob somewhere onboard with all twelve copies of a certain book in front of him putting in revisions. Every revision and update is reviewed and signed for by several people, up to the department head. Somebody signs for installing the update. Reports are filed. Reviews are done. It takes time. I was a nuke, but the quartermasters go through the same thing.

I agree the system needs to be modernized, but these things take time. The USSR came out with a new class of submarine every time they came up with a new idea. The result was they didn't have parts for anything and none of their boats could stay operational for long. The U.S. builds lots of the same type of each submarine and upgrades them as a group. They make absolutely sure that the change is good for everyone, they upgrade one ship, test the crap out of it, and if it works they upgrade all the others. When I got to the USS Albany in 1990 reports were hand written and there were only one or two computers on board. We used cabinets full of microfiche. When the USS Greeneville was built in 1994 it had workstations throughout the boat and a bank of CD drives with all drawings etc accessable from anywhere. As older boats went into refit they got upgraded to computers. It takes years, but the Navy doesn't rush anything until it is completely vetted. Heck, I toured a WWII submarine and it used the exact same oil purifiers as the newest boats in the fleet.

As for the crew, they get lectured about complaceny all the time. There is a reason. When you have so many things to keep track of its easy to let some of the mundane stuff slide. Thats what always burn you. The maps should have been updated. The quartermaster should have warned the OOD, and if ignored he should have gotten his LPO out of bed. There were half a dozen people in Control who could have / should have seen a problem and asked questions. But it becomes routine.

Fast Attack Submariners don't do very well with routine. They have so much to do that the most basic things sometimes seem to get in the way of trying to catch up on other work. But when the fit hit the shan they knew what to do. They saved the ship and their fellow crew members and returned to port under their own power. Mistakes were made and, correctly, many people will pay for them. There is no room in that world for second chances.

I've said it for years and it still true:
A fast attack submarine is the best place to work in wartime, and the worst place to work in peace.