Poorly charted water. A coral mount that wasn't supposed to be there, but was. The fathometer won't warn you about those. (And neither will sonar).
And how does a submarine free itself - can you just put it in reverse?
Yep. Blow ballast tanks and backup --unless you think you breached the pressure hull, then you stay put and wait for rescue.
Wouldn't that be obvious, quickly.
an airedale