I had those on my GSM-1and GSJ-1. As Fretworn says, It’s a pin used to keep the fretboard in place when it’s being glued and clamped. It’s not rocket science to put them where they don’t interfere with the nut. Just simple carelessness.

You can grind it away with a suitable Dremel bit, or you can mark the position on the nut and make a small cut-out for it so the nut sits level.

In theory you could use a small file to level it, but you are far more likely to make the slot floor uneven instead.