It looks like it might be a simple case of moisture under the sealants trying to escape. The sun pounding down on the roof is heating the glues and sealers under. Simple evaporation to dry the glues is attempting to occur. With no where for the gasses to escape, they are forming bubbles. I don't think you have anything to worry about.
My Springdale did this all the time, the bubbles came and went, for about 5 years when it finally quit.
But, just to be certain, check it often for leaks. I think you're OK.
