So, I haven't picked up on any whispers because I have to play with my sound pretty low most of the time. That said, it might actually be a callback to Sands of Time. In that game, every save point infused Prince with the sands of time such that he could see the immediate future. While that played out, increasingly loud whispers complemented the preview of things to come in the story. I think the whispers occur elsewhere, too, but that's the part that comes to mind for me.
The only time I've noticed 'whispers' is when finding and opening one of those sands of time jars, so you're probably right on the money.