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That is not normal. It looks like some separation of the decking under the membrane. The roof should be flat, smooth and no bubbles.
A 2011 should be in warranty. Take it back and tell them to redo the entire roof.
Amateur Radio Operator (KE5DFR)|Full-Time! - 2012 6.7L Ford Crew Cab Dually -2013 HitchHiker Champagne 38RLRSB - Travel with one Standard Schnauzer and one small Timneh African Gray Parrot