I had the same issue as the OP and a few of you guys with a leak in the roof of the house and the garage.
As some of you said, there were no shingles bent, damaged, lifted or anything. In both of my cases, the leak was coming from a nail that was installed underneath where two shingles came together.
You would never have see it from the ground, or even when you were up on the roof. The only way we determined where they were was to measure the locations of the leaks from inside the house, and then take those measurements up onto the roof and start looking in the locations from the outside.
When no noticeable damage was found, we started to lift the tabs of the shingles up slightly in the areas where we thought the leak was coming from, and sure enough there were nails installed directly where two shingles were butted up next to each other.
It took a few years to start leaking after the roof was installed, but eventually the water running down the roof and between these shingles right over the nails found its way down inside the house and garage via the nails.
We repaired the leaks by first caulking over the nail heads, and then putting in some cut off tabs from extra shingles under the area where the two shingles came together, and over top of the nails.
Because the extra tabs were installed under the existing shingles you could not see them, which was nice because even though the extra tabs were taken from the same batch of left over shingles, the shingles on the roof had changed color just a bit from the sun and dirt and stuff that gets on a roof.
Jim