A few times I had to do this, I used a non-permanent red sharpie, with which I gently dabbed the non-emulsion side of the negative. It prints as a softer, fuzzier white hole, and so it is then relatively easy to spot on the print. Naturally, this is easiest with LF negatives, but I have done it on 6x6. Some negs have a better non-emulsion surface texture for this than others. In my experience, HP5+ and Tri-X are easier, TMax a little harder, for me. After printing, the red is easy to wipe off. Please let me know if you think that I am doing something bad to my negs this way. You can always sandwich another, blank negative on top of yours and place the spot on it, effectively creating a very simple negative mask, just watch out for newton rings with some films, like TMax.
You can also remove the spots using a very sharp surgical blade, by very gently dabbing the surface, not scratching, but it leaves a mark that is visible, on glossy paper, when you look at the print at an angle.
As for why you got it in the first place, the most likely reason is dust or sand on the film during exposure, but sediment in your processing chemistry can cause those too. Some people blame film defects, but I have never felt that was the reason in my case.
Anyway, get used to dealing with this issue, as it will keep happening—especially in the smooth tone areas like sky, as it is most visible there.