What is this? Vycor Plus as flashing?

So we have a new roof. Paid 5600 to a company who did it. I sent a neighbor who is comfortable with heights to check out something we thought was irregular, but it turned out not to be, he found other things though.

We don’t know what to make of any of these findings. If these things were done wrong or right.
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Or this

Or this

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What’s in the ridge vent?

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Leak to be?

Around the skylight

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All the edges look like this

There’s a nail in the vycof

Vycor plus spec sheet

1.exposed nails needs to be caulked
2.upper corner of skylight might need to be reshingled,so apron peeks on bottom part of shingle if its velux,if just all soldered single piece skylight then solid bead of caulking all around skylight.
3.vycor probably was applied ebcause installer thought it might give extra protection ,underneath there should be aluminum flashing,which is more than enough to hold it waterproof.
4.ridge vent ending is bit off,but nothing to worry about.
5.counterflashing looks correct except using clear caulking instead of fresh mortar.But its ok for 5-20 years.Depends on silicone type.
6. felt paper under ridge vent is probably just a single piece wasnt cut and left hanging.nothing to worry.

I imagine the vycor is old and wouldn’t come off
The previous installers likely covered the front of the flashing.
Nails in the joint are crappy. Overall otherwise looks like most roofs, not perfect not terrible

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Looks to be re-used. The 2 open nail holes towards the bottom of the pic might be a problem?