Does it leak where the repair is? Can you see where the water is coming in? I would be more concerned about the leak than the bubbles in the rubber.
Yes, it does leak where the repair is, the caulking wasn't done properly, and my hands are tied until I have a determination on the repair that was done (if it is a good quality repair or not). In actuality, the repair was never done. Just a new rubber membrane put down. The repair was supposed to include new plywood (or luan) BEFORE the new rubber membrane was put down. Trust me when I say there is more damage to the unit now than there was from the actual tree strike.