Blisters in New Rubber Roof - Need quick answer


I am re-roofing my house. On the two rear corners are small (10x12 or so) flat roofs covering additions. These have given problems from day 1 in spite of having been re-done twice with tar and gravel.
This time, I wanted to cure the problem and elected to go with a rubber membrane system. Upon applying the membrane, there were small blisters (1"x2" or so) all over the roofs. The contractor said that this was due to heat buildup because of the glue and that they would go down overnight. They didn't. When they applied the membrane, I don't think they used a roller to force air out. This is early AM, and I don't know yet what they will be doing today.
What should I think of this, and how should I handle it?
JFM
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JFM wrote:

He said they'd go down, they didn't, tell him to fix it.
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dadiOH
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