HVAC supply lines and curbs with leaks at the membrane

 Tears and holes in curb flashings allow water to penetrate the membrane and deteriorate the insulation board causing puddling and more significant leaks and insulation issues

In this photo, you can see signs that water and debris gather in the sagging area in front of the roof hatch.  This area appears to have been leaking for a while, and some repairs have been attempted.

Here, you can see where the termination bar was used to flash this chimney area.  The fasteners are beginning to loosen, causing movement and sealant failure.  There does not appear to be a reinforced perimeter strip at the lower change of plane, allowing more movement and trampolining in this area, making it much more likely to move or tear.  This area appears to have some leaking issues.