The root system of moss grows up between the shingles. This causes water to wick under the shingles resulting in rusted nails and water penetration into the roof. 

As you can see, the arrows point to numerous nail pops all along the ridge cap shingles and other places throughout the roof.

This pipe boot was installed by just ripping a hole in the shingles, and on top of that, it’s not nailed down, letting windblown rain penetrate the roof.  

Rotten tree limbs broke and scattered across the roof, causing superficial damage to shingles. At first, I was sure this limb had punctured the shelter, but luckily, it just scraped it up and messed up the tabs on the dimensional shingles. The pictures at the top will show some of the damage.

One of the pieces of roof decking has popped up and freed itself from the nails. This has lifted the shingles just enough to let the wind in between the 2 layers, further breaking more shingle seals. The bottom picture shows a rusted nail, so water is getting under the shingles. 

This rain diverter is flush with the shingles that it’s up against. This can allow water to back under the shingles. It should be installed on an angle shown here as the red line.