Small rib /"Ultra rib" new roof but see penetrations on leg of panel

Just had an install, but after first rain i saw water coming out under metal panel above eavedrip, and check bottom screw in pan and it is a litttle loose, you can flex the panel. easy fix to just screw that in tighter. Seems like the washer is not out to the edge of the screw head and seemed higher. BUT after looking at where panels lap i can see predrilled holes at the bottom of the panel under the overlapped panel. The entire roof is installed and I will look for more but I did see one other the same. It seems wrong! I should NOT HAVE holes in the metal. I will look tomorrow for more. It is 11 p.m. now. note-screws are installed over battens/shingles in the top of the overlapped panels. This was a licensed roofing contractor. Should I pay the balance?? Should I let the final inspection proceed? Should I contact the metal supply company? Should I have the roofing contractor remove the panels to see if it is installed all the way up??? The young guys installing were never visited by him during install. There were plenty of extra panels left if the 2 I did see were not needed. This area was the final area installed. Also there are no bottom closures and I did not notice til almost done.

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I was thinking this was their "marker" for the legnth of the overhang (Ie..2 or 3 inches) but they are not consistant. some are at the edge and some penetrations are 1 1/2" away from eavedrip. hmmmmm???? Any ideas?