Sean, I too recently got 2 yds of the same 2.5 oz/sqyd Climashield Apex from thru-hiker just last week and noticed the same thing as what you describe. However, as evidenced by some of the post's here already, it looks like it is a normal thing. Also, with my limited history of ordering from Thru Hiker, as well as the many others that use his materials and praise his stuff, I feel like if it was not acceptable, he wouldn't have shipped it. Just my thoughts.
Anyway, good luck with your quilt!