It is not unusual for the rubber roof membrane to develop small bubbles. They should not significantly increase in size or cover a large area. Recommend you show your dealer on next visit, to document or send photos to Thor. (Just in case it becomes a problem).
My prior MH, 2000 GeorgieBoy DP had some bubbles and they never changed or caused a problem in over 15 years... Roof material was made by DICOR and they warned- do not puncture the bubbles and try to re-glue. The roof material should have a 10-12 year warranty.
Enjoy the new RV..