I noticed that as I play in the Village and Fields area, not only does the game auto-save but also auto-deletes some auto-saved files as well. Or can it automatically overwrite them? Is this a glitch?

Since some patch, or the Enhanced Edition CD Project integrated some auto-delete/overwrite feature.
I remember having read in a review of the game, that the reviewer complained the game would create loads of auto-safe files that would grow really large on the hard-drive as well by numers as by size.
So It´s safe to say that CDP Red just patched that.

I see. Good to know.

Yep, I can confirm, there's a finite amount of auto-saves and quick saves. Best to use plenty of manual saves to supplement it.