Whenever that happened I would load a previous file to fix the issue and it also fixed itself once as you said, so I'm not hearing it anymore.
I've tried going back to a few places where I think heard the bug sound but I don't remember where they were.
I've looked in the Audio->BGM files and I think it's the DarknessHere sound effect.
Another thing, I've found this spot here and I think it wasn't intended to do what it did.
That water spot teleported me forward into the game after a cutscene, teleporting me inside of the Succubus Castle(I think?) between the 2 towers.
That made me skip like 5 or 6 fights so I guessed it's another bug.