I would suggest to remove the nail and put a urethane sealer which can be found at any home store to seal the hole from underneath.
How to seal roof nails.
I ve always considered it necessary to caulk any exposed nail heads on a shingle roof there shouldn t be many.
Don t worry if the glob looks a bit thick.
They can also be used to apply insulation board and felt to wood substrates.
The nails might have popped.
Fill small nail holes with silicone caulk or roof cement.
If your ceiling has a plastic vapor barrier between the drywall and the attic insulation push the insulation aside and look for flow stains on the plastic often water runs to openings in the vapor barrier such as at ceiling light fixtures.
Remember to seal over the nail heads.
However they can cause leaks particularly if you have an asphalt shingle roof.
Roofing nails sticking up called nail pops might look like an unimportant issue.
These grip rite roofing nails are for installing asphalt these grip rite roofing nails are for installing asphalt roofing shingles.
I must admit i ve seen many builders that do not seal the nail heads.
The shingles are asphalt backed and this asphalt forms an adequate seal around the nail.
They are electro galvanized to help resist rust and corrosion.
Some roof leaks are tough to locate.
For loose nails that have yet to push through shingles you can lift up the shingle and hammer the rising nails back down.
Remove nail lift shingle and apply a small dab where nail penetrated shingle then push the overlapping shingle down and your done.
Apply a glob of roofing cement to the spatula or putty knife.
Repeat these steps for each of the exposed nail heads.
Sometimes the water shows up at a ceiling spot distant from the leak.
The claim was that nails have to pass through a minimum of two layers of shingles.
Alternatively or in addition you can drive a new nail nearby for a fresh stronger hold into decking.
Smaller nail holes will be permanently fixed by this method standard roofing nails would be either 3 8 inch or 1 2 inch making a hole.
It will smooth out once it dries.