In this photo, you can see a framing nail sticking out of the roof, causing the shingle to be displaced and leaving a hole that almost certainly is leaking. The nail was removed, both shingles were lifted, holes repaired, and sealed back down. 

In this photo, you can see that the ridge caps shingle hers suffered an impact of some kind and could potentially be causing a leak. This was sealed up with roofing caulk.

Here, you can see that the last ridge caps it was installed left exposed nails. These should be sealed with caulk to prevent leaks. This area has now been sealed.