Rubber roof bubbles or blisters

Yes, I had them and they did get worse. I punctured them with a hypodermic needle filled with bonding glue, then put a weighted flat board on it so is adheared. The problem is the adheasion can be a problem if under the material there is moisture and or mold growing. Some units were recalled due to bad factory instalation and were recalled for repair. Mine did not happen until the roof was 12 years old. Last year I replaced the entire roof with DOW hot shot 3/16 inch roof at $136 per linear foot, mine was $4700. Now it's a 20 year roof, and no more caulking,as they spray over flanges and front and rear caps.