There are a couple of things that can cause those black spots.
1) Bran oxidation (very common).
2) Oxidation of the iron in the flour that is part of the flour enrichment blend (enriched flour).
Spots are generally characteristic of old flour and caused by bran oxidation. It doesn't really affect the baking so much as the flavour is not as good but it will not hurt you.
I have also noticed that this can happen if you have not cleaned your oven in a while and there might be a buildup of fat on top and sides of the oven if you have been roasting or broiling food lately.