Some lower quality roofing the color is sprayed over the granular after the granular is applied, where higher quality roofing applies a colored granular. It is natural for the granular to roll off the shingles as they age (just look in your gutters). Sometimes it appears as some kind of staining occurring in random patterns, but your usually just looking at the 'unpainted' side of the granular that has rolled over. Usually it is not an issue, just a downside of this manufacturing process.