This picture shows that the pipe boot is not securely screwed down to the roof. This can allow blowing rain to penetrate the roof

Flying squirrels can get under the ridge cap and enter the attic through the ridge opening under the cap. Foam closures were never installed when the metal roof was put on. Here is an example of what it should look like under the ridge cap when the closures are installed. 

Here is what the ridge cap looks like now. There is nothing under them. It’s just an open gap. I shined my laser pointer under the ridge vent, and nothing was in there. 

The ribs on the metal panels will allow small animals to go in and out of this small hole.  Here is what it looks like

we will fix this by stuffing steel wool in each hole and then filling them with expanding foam

This open pipe vent can let animals crawl inside of it and, if not adequately secured, get into the attic, or worse, die from not being able to back out the pipe. the thing sitting on top of the pipe is a birds nest  
to fix this, you would want to get some 1/4 inch chicken wire and screw it in place over the opening of the PVC pipe to keep any critters out.

Due to the snow, it was impossible to get on the roof, but I found a few screws starting to back out, so I would say it’s like this where it’s leaking as well, so a roof tune-up in this area.