The most common explanations given for the phenomenon you described are dead yeast cells or the oxidation of bran in flour. It might also be yeast that was not properly incorporated into the dough. I researched this subject some time ago after I noticed spots on the surface of my dough balls. However, my dough balls were a lot older than yours (I call them "geriatric" doughs). You can learn a bit more on this subject by going to http://www.pizzamaking.com/forum/index.php/topic,3985.msg41385.html#msg41385
and also by reading some of the following posts in the same thread. You should specifically look at the photos linked in the above post to see if your dough looked like what is shown in the photos of the dough balls I posted. If not, it would help to see photos of your dough balls. It might also help to know more about your dough formulation and the way that you prepare and manage the dough. I concluded that the spotting occurred with high-gluten flour in my case, and not weaker flours.