Hey ggoguen, welcome to the forum. Were they blisters or air bubbles? If they are air bubbles I would take it back and see if they could apply more adhesive to the underside and stretch it back smooth.
In my way of thinking a blister could be a sun or heat caused blister in the rubber material. Whereas an air bubble is under the rubber and is a pocket of air between the rubber and the wood roof. Just semantics. It really doesn't matter. If it is a pocket of air I would take it back and see if the dealer can raise the rubber and reapply the adhesive and stretch it back tight. If there was a problem with the rubber material itself, you would probably have an issue with the manufacturer of the rubber. Having said that, I don't recall anyone having any problems with the rubber roof material.