Bubbles of air are unsightly but won't cause the membrane to fail - so that's good news.
The bubbles are trapped air or moisture. These can be caused by a variety of issues which are all avoidable if the roof design is correct and the membrane is correctly installed.
The most likely causes -
Vapour from Contact Bonding Adhesive
Nine times out of ten the issue here is not letting the adhesive become touch dry before bonding the EPDM
The adhesive is solvent based and must be allowed to gas off and become touch dry prior to bonding the membrane into position. When the rubber membrane is bonded too quickly, and prior to the adhesive drying, bubbles will appear under the membrane caused by the trapped vapour from the adhesive.
In time the bubbles will decrease as the membrane is partly breathable.
In the most severe cases the membrane may need to be peeled back and re-bonded.
Expanding Trapped Air Within The Roof Structure
This is the other main source of bubbling - it can occur on warm deck roof designs where the EPDM membrane is fully bonded onto either a timber deck or directly onto the insulation.
Dryness is a must for EPDM installation - this means the underlying timber structure as well.
If the roof structure under the insulation is damp or the boards are fitted with large gaps the trapped moist air will expand when the temperature rises and appear along the seams in the boards.
You may see this issue come and go with temperature rises and falls often the membrane will contract back in to position..
Check the roof deck for gaps between the boards - pre installation fill with an expanding foam adhesive to help seal. A visqueen membrane can also be installed under the deck to keep any expanding air at bay.