I’ve never seen dark spots like this in the roof? It doesn’t appear to be causing any issues but id love to know what it’s from
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They look like they align with where the nails would be located underneath the shingles but I have never seen them bleed through like this.
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Got hot in bundles and the adhesive strip pulled off granules is my guess.
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I agree with Dave that it looks in alignment with the nailing. I wonder if the nails underneath have popped causing a little more pressure and “thinning” the shingles some.
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I also agree on the nail theory too, but another possibility could be a defect in the shingles.
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It looks like the roofer didn’t adjust his nail gun properly, leaving the nail heads slightly above the surface of the shingles, the roofer’s foot traffic may have scuffed off the granules. 
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My 2Cents…Manufacturing issue.
Hi Scott.
That would leave a visual protruding bump atop the shingle or even lift the shingle slightly.