It can't be on the negative, because I've made 4 prints now and the spots are in random places. My darkroom door isn't perfectly light tight...I can see a bit of light in places around the edge. But I consider it light-tight enough to work with paper in there in the daytime. If there were light leaks, I don't see how they could be focused onto an image that would give small spots. I would expect general paper fogging. And besides, the worst print so far was made last night when it was dark even outside the darkroom. I made the exposures through an Ilford under-lens filter, but there doesn't seem to be any pinholes in the filter. I suppose a tiny pinhole could expand into a 3mm light spot on the print by the time it got down to the baseboard.
That looks like a flaw in the negative that doesn't show up with smaller enlargements. I wouldn't worry about the paper so much. One things for sure, it's not a light leak.