Blisters on an almost flat roof may be caused by heat and sun, but they often signify moisture under the surface. The chances are good that water has penetrated the roof membrane through a nearby hole or flashing.
If there are several blisters or the blisters are quite large, consider calling a roofing contractor to handle the work. Otherwise, follow the steps below:
1) Sweep gravel and dirt away from the blister.
2) Using a utility knife, slice through the top layer, releasing the pressure from the bubble.
3) Feel inside the hole for moisture. If it feels wet, look for possible sources of leaks along the flashing or in the same general area as the blister, and fix those leaks.
4) With a putty knife, work plastic roofing cement into the pocket and around the surface of the cut. Apply cement beyond the damaged area at least 2 inches in all directions.

5) Cut a patch from an asphalt shingle or a piece of roll roofing that’s about 2 inches larger than the hole, and slide it into the slit. Press it into the roofing cement, making certain to cover as much of the area inside the cut as possible. Cover the blister or hole with roofing cement to seal the patch, and then apply cement about 2 inches beyond the edges. When the cement begins to set up, sweep the gravel back over the top of the patch.