This seems to be becoming a common complaint. It's not strictly necessary for every inch to be bounded to the substrate, but it sure speaks to the quality of workmanship when it is not. And a big bubble will lift as you drive at highway speeds, due to reduced air pressure over the roof.
If it bothers you, slit the material and squeeze in some adhesive and glue it back down. Then cover the slit with lap sealant or Eternabond tape.
2004 American Tradition; 2014 Buick LaCRosse
Homebase in the Ocala Nat'l Forest near Ocala, FL