New roof install. Flashing issue

[jpkluczka]

I had a new roof installed on my rear dormerd cape. Im not too impressed with their work. The flashing was nailed down in the back of the house using thin nails. I know enough to know thats not a good thing. I covered the nails with white screw caps using clear urethane caulk. As you can see its laying pretty flat but i am worried about wind driven rain and snow getting underneath. they also missed the wood near the peak nailing down a shingle, i have them coming back for that. Also the valley where my chimney is is uneven. Could it be because the area sits in shade and hasnt had time to set yet?

 

[oldognewtrick]

The shingles should be laying flat beside the wall and chimney. Call them and have them come back and fix the lifted shingles and replace the drip edge they nailed through.

 

[jpkluczka]

so i showed them the side by the chimey. They said its wavy because new flashing was installed and it should settle down. Im not convinced. Its been a week already. It looks sloppy to me. Does it look like it will leak? I have the headwall flashing sealed up real good. the nail covers with the urethane caulk underneath. My worry is water getting in underneath, which as you can see in the pictures it is pretty flush. I really dont want to open any more can of worms. Either way i know where this is going with them. I just dont want leaks. Thank you for the response

 

[joecaption]

Just going to have to make some guesses because I'm not there.
To have installed new flashing at the bottom of the dormer the siding would have had to have been removed.
If it done right there would have been counter flashing installed before that exposed metal flashing was installed and there was 0 need for any exposed nails.
That picture of that area between the wall and the chimney has me really worried.
Sure looks to me there was issues going on that should have been seen and fixed once the shingles and paper was removed!
That whole are looks like it is sagging.