With over 20 years of Navy experience I can say you are mistaken. Things have improved since I first joined the Navy but we (humans) have far better and more comprehensive maps of the surface of the Moon and Mars than we have of the bottom of the world’s oceans.
Hell, I’ve used charts where the only survey of some of the area happened over 200 years ago with the rest being a big fat unknown.
There’s only so much Hydrographic survey capability in the world and the worlds oceans are a massive and changing place.
Unless the submarine is running around banging away with her active sonar (negating the point of being a quiet stealthy platform), no sub is going to detect a mountain that isn’t on her charts except by running face first into it.
...........well, your Navy experience exceeds mine by 13 years.
That said, what’s your best guess about what happened or do you believe the Navy version?
Your assertion that underwater mapping is not comprehensive or perfect is well taken.