There is no reason for you to accept something that doesn't work as intended. The builder owes you a new membrane.

That is ludicrous. It needs to be recovered. Do NOT allow them to continue roofing until this is remedied. As someone who has gone through a similar issue, this is not an area to take shortcuts (time or money). Your builder is doing you no favors to fix this issue...he's doing his job.

Metal roofing is similar to tile roofs where you are highly dependent on the underlayments to keep the sheathing dry. It's not from physical water such as rains, but from moisture that can build up. The underlayments act as a drainage plane where the water runs down and out at the leading edge of the roofing. Tile has a weep screed flashing at the front edge while the metal roofing is dependent for run off through the seam channels. You need to insist that the underlayments damaged are replaced or properly repaired.

With exposed fasteneers, you are going to want to make sure the installers know how to correctly fasten the panels. Too much pressure will wear the gasket prematurely, too little pressure will allow water penetration. Most pros use cordless impacts that have an adjustment to get the fastener to the correct "tight".

Thanks for the great tips.
Will need to chat with builder in the morning.

Definitely have the membrane replaced in the dmged areas, I work as a Catastrophe Insurance Adjuster and have seen numerous metal roof's leak as result of poor or improper installation, get what your paying for.

Thanks again!
Seeing that some holes may have likely happened with a ragged snow shovel, how likely is it, that there are lots of tiny holes that the workers may miss?
I wonder if it requires new blueskin OR maybe small holes seal themselves up ok?
Meeting in the AM. NOT looking forward to this one.