Probably some anodizing broke loose from the inside of the tube, it happens. I have had several scopes develop some internal debris, from a $300 SS to a very expensive USO last year. You can take it off and smack it on a phone book to see if it dislodges. Bad thing is that it can come back and dance around inside. I have to say that it would bother me and I would send it back, especially on an upper end (expensive) scope.
When the particles are in focus like that, they are on the glass reticle. Unusual with Nightforce - not surprising they offered to fix it. More common with USO, because of their assembly environment and processes. Back in the day of wire reticles, this stuff didn't happen.
That is surprising that it showed up like that. I had the same thing happen with a zeiss and they wanted to charge me $400 or some crazy number like that to fix it. then another $50 to ship it back after repair... or they would ship it back unrepaired for free... I took it back. Nightforce is a much better company to work with.
Not to get on the Zeiss bashing, but I had a 3-9 Diavari-C that was on my .340 Weatherby for over 20 years, and it seemed to stop holding the zero. I sent it back to Zeiss, and they replaced the tractor spring and returned it to me, no charge. When I looked through it, there were several black specks in the field of view near the crosshair, similar to what the OP has in his Nightforce. I figured that if they screwed that up, what else did they miss. I sold it, and got a Zeiss Conquest 4.5-14, and that never seemed right. Field of view seemed "tunnel vision", and focus wasn't crisp as I expected. I sold that and now have a Swaro 3.5-18 with BRH, and love it. Zeiss seemed to fall a little in the QC, IMHO.
I understand that another company (Minox or something like that) services the Zeiss scopes that are returned now.