Here in Texas, where the temp on an asphalt shingle in the summer time could reach easily 140 degrees, we also have some staining on these shingles.
I once asked the roofer re roofing our roof after a hail storm what that running stain was. He replied that during the manufacturing of these shingles, sometime a metalic substance or a type of rock gets in the batch and will cause the shingle to stain. It gets worse in the Spring and Fall when the humidity and rain are more frequent and the stuff is actually rust. It will look just like a person that just hung a nice fence with non corrosive fasteners and the nails started to bleed.
He then told me that this was under the warranty of the manufacturer. Now, that is one story and one in maybe a complete different atmospheric condition part of the country.