What kind/type of yeast are you using? From the photo that you provided, it appears that the spots are all about the same size. If flour or fat were the culprit, I would expect to see a more random size pattern formed, but because of the uniformity maybe we need to be looking at the yeast, especially if it is ADY or IDY, and how it is added.
We make a VERY undermixed Chicago cracker type crust that resembles a pie dough rather than a pizza dough (just 45 to 60-seconds of mixing time) In this dough we see a lot of flour lumps but they have a very randon size distribution and they are hard when squeezed, and when broken, you can identify the flour, this is why I am leaning away from the flour in this case. However, it might be dried dough pieces from a surface that the dough was scraped off of at some point, just a thought.
Tom Lehmann/The Dough Doctor