Were these shingles installed over an existing layer of shingles, or was the roof stripped to the sheathing?
Hopefully the latter.
Still, I agree with David. Let the sunshine and see if that settles them a bit. Still, I'd document and notify the roofer.
If these shingles were installed over another layer of shingles, that pretty much voids most shingle manufacturer's warranties. Then again, shingle warranties aren't good for a whole lot anyway.
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