Exposed nail heads under metal roofing

I recently had a metal roof installed with a galvalume product from Tri-County Metals. Since that time, I have noticed bumps in the surface the metal roofing, shown in the following pictures.

So far, I have found about 30 such bumps on the surface of the roof.

I have talked to roofing contractor and he has come out and made repairs on multiple occasions. The appearance of the repairs look like nothing has been done and the bump are still present, or it looks like they were hammered flat.

So, I inspected one of the areas that he has claimed to fix and found a nail head protruding above the surface of the batten about 1/8 of an inch, directly below the bump on the surface of the panel.

So out of curiosity I open up a small section over my breezeway and that a good number of the nail heads are above the surface of the battens.

I have spoken with three representatives from metal manufacture they have all told me that this is unacceptable and would void the warranty. However the contractors attorney is stating that I don't know what I'm talking and they have also talked with the manufacture and I don't have anything to worry about. I have naturally asked them to have the manufacture put it in writing and provide it to me but they have and have only increased their threats of legal action.

So my questions for you are as follows:

1. Is it okay to install metal roofing, on top of nails that protrude above the substrate surface as pictured, without voiding the warranty?
2. Are panels repairable that have damage that is caused by protruding nail heads, without voiding the panels warranty?
3. If panels are repairable and do not require them to be replaced to maintain the panels warranty, what is an acceptable technique to repair such panels?

Thank you for your time.

I have two of them referred me a line on the warranty card that says "Deterioration to the panels caused directly or indirectly by panel contact with unsuitable fasteners and sealants." Another person answered the questions that I posed above and said it was not okay. I have told the contractor and his attorney yet they are still insinuating that this is okay. So I am wanting to the perspective of other professional or individuals with knowledge about metal roofing and their installation.