NEW construction home has no flashing on chimney?

moved into home a year ago and now we have a leak in a room (which is near the chimney line). Our builder's defense was that there's "internal flashing". But from what I've researched, there's no such thing. I also have 4 exposed nails in the shingles which could also be source of the leak. My question is - is this bad workmanship? Negligence? I also have a deep "valley" in the rear of the chimney which you can see in the second photo. Wouldn't a good roofer create a saddle/cricket so the water can properly run off the roof?
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