It could have been me, but I'm 99.9% sure I haven't done anything to the frets (yet). I know I straightened the neck when I got the bass notched edge but I think that's it. Pretty sure I didn't level the frets as I was going to do that later.

On a proper wooden neck, scraping the wood with a single-edged razor blade is a good way to get the wood smooth and remove marks like that. I've just been doing it on a Les Paul Signature where the fret files made similar marks near the frets and it got rid of them nicely.