Snow Bar Screws

I just had an Image II standing seam roof installed on my house. The contractor recommended snow bars due to the occasional heavy snow fall in the area.
The snow bars were installed on top of the standing seam with 1-3/4 " screws which screwed into the roof deck. The workers installing the snow bars carelessly installed the screws at various angles resulting in penetration of the male portion of the roof panel profile thus exposing leak paths to the underside of the roof panels. The contractor has stated that the roof will not leak and not to worry. There are potentially hundreds of screws that are installed in this fashion to the point that I think the roof needs to be redone. I have even built a mock up to prove that the panels will leak through the screw penetrations.
Has anyone had a similar situation and how was it resolved?
These slow dripping leaks may not show up within the contractors warranty period but they will surely appear after major damage to the roof decking.
The best part of this is that the contractor says that the roof was installed correctly to LOCAL PRACTICES!

I had contacted the manufacture on a related issue of not having ridge and hip closures. The response was that if is water was repeatedly allowed to get under the panels then they would not warrant the finish.
I have attached an image of the screw installation.

Thank you Eric, you have confirmed my belief that this was wrong.
I have reached out to the manufacturer with these pictures and have a verbal confirmation from them as well.