was this installed correctly?

I have a new metal roof It is a McElroy Meridian 26 Guage and the installer messed up a handful of things and I have two items they are clamming are not issues as "it happens to all metal roofs" or are due to existing conditions. the first one is denting on the bottom where they bent the panel up I am being told this is normal and not an issue. the second is the bottom of the panels do not line up and appear angled in some spots. I am being told this is due to the unevenness of the plywood behind but I can't figure out how this would cause the bottom that goes past the plywood to be at different spots.

is this true for metal roofs or is the contractor trying to get out of replacing bad craftsmanship?

Thanks!!!