Have them take that metal off that they installed "over" the existing step flashing. You'll need to check the step flashing cards to make sure they are all aligned and in the right places. Chances are they are not. If they are in the right places then it's your window leaking. Best I can do for you without running a hose on it. 

No you could run a hose on it...start along the roof line first and eliminate each area before spraying up towards the window. 

Yes we have siding positions open and hardy siding installation open please call and stop in our office/showroom

hardie board has a 30 year warranty, why are you covering it?

yes

It appears that you are missing both step flashing (between the roof and the wall) and the head flashing (above the trim running parallel to the roof line). Here is the link to the Hardie Best Practices manual with specs on both flashings: https://www.jameshardiepros.com/getattachment/9a1017e1-853d-4574-b3e9-7afb1a5a472d/intro-tools-hz5-us-en.pdf. 

That is a gable vent, they help cool and dry the attic