What do exposed or raised roofing nails mean for repair scope?
Isolated, repeated or associated with damage?
For one identified fastener, ask the roofer to explain the repair to both the attachment and the surrounding water-shedding layers. An apparently small defect can still require careful handling of adjacent shingles. A blob of sealant is not evidence that every necessary part of the repair occurred.
For repeated raised nails across a roof area, ask for a broader assessment of attachment practice and the condition of the material receiving the fasteners. Do not accept a remote diagnosis of roof-deck failure solely from the number of marks in a photograph.
If the fastener is near an active leak, damaged shingle or roof penetration, those conditions need to be considered together. The nail may be relevant without being the only water-entry path. Ask which findings support the proposed repair boundary.