Never seen ones just like this before… Looks like wrinkles, but it only shows on the lower layer, and not the top.
Couldnt get on the roof to investigate, had to use drone. (New build, not allowed to walk roof)
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Looks like a manufacturing defect.
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If I had to take a WAG, it is wrinkled underlayment. It does appear to show through the upper layer, just not as pronounced.
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That was my thought, too. Just odd. Looks like a rope under the shingle. 
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I would agree except the same anomaly is visible in multiple areas in the OP, my WAG is the same as James’, defective shingles.
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by the size of the bird droppings they must have pterodactyls in your region lol
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Small shingle cuts/strips gets into the batch.
It is then double ply at those areas.
It is just cosmetic.
Manufacturing defect.
You see nail heads? I count 5 fasteners or something similar.
Roof inspected by: Drone
Limitation: Could have walked the roof but didn’t want to die from excessive exposure to bird shat.
Recommendation: Kill every bird within a 5 mile radius.
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The roofer should have culled out the bad shingles.
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Seagull shit.
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