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.
Repeat these steps for each of the exposed nail heads.
Apply a glob of roofing cement to the spatula or putty knife.
Sometimes the water shows up at a ceiling spot distant from the leak.
They can also be used to apply insulation board and felt to wood substrates.
Roofing nails sticking up called nail pops might look like an unimportant issue.
Wipe the glob of roofing cement over the nail head.
The shingles are asphalt backed and this asphalt forms an adequate seal around the nail.
Make sure the roofing cement extends to each side of the nail head covering it completely.
Alternatively or in addition you can drive a new nail nearby for a fresh stronger hold into decking.
Remove nail lift shingle and apply a small dab where nail penetrated shingle then push the overlapping shingle down and your done.
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.
The nails might have popped.
Don t worry if the glob looks a bit thick.
These grip rite roofing nails are for installing asphalt these grip rite roofing nails are for installing asphalt roofing shingles.
They are electro galvanized to help resist rust and corrosion.
The claim was that nails have to pass through a minimum of two layers of shingles.
However they can cause leaks particularly if you have an asphalt shingle roof.
Fill small nail holes with silicone caulk or roof cement.
Remember to seal over the nail heads.
Some roof leaks are tough to locate.
I heard an opposing opinion recently.
It will smooth out once it dries.
I ve always considered it necessary to caulk any exposed nail heads on a shingle roof there shouldn t be many.