Call the roofer and if unsatisfied with the response, the manufacturers of the shingles and upgraded underlayment.

What is the spacing of the roof trusses/rafters, and how thick is the roof sheathing?

When there is apparent buckling in the roof plane it often means widely spaced trusses/rafters with insufficient thickness of sheathing.

Another possible cause could be that the roof sheathing was allowed to become saturated before the water resistant barrier was installed.

Or both.

My builder is out of town so I’m not able to ask him. Here are a few pictures. I hope the pictures answer your question on spacing. Thank you both for taking time to look.

More pictures

Your photos answer your question. Look at the underlayment in the last photo - see where it's wrinkled/buckled? Now look at your shingles in your first photo and see where the wrinkling/buckling is occurring?

Looks like an underlayment problem. Not decking, not shingles.

Thank you everyone for the quick responses! I thought that may be the problem but wanted to make sure before I ask builder.