Most of the time the bubbles are really just sawdust, staples and debris that was left stuck in the adhesive before they laid the rubber down creating the bubble.The pics posted appear to have small spots, not to worry unless they get very large or penatrate the roof membrane.
Edit. The most important thing while you are up on the roof, check all the roof caulking for cracks or areas that look like the caulking is coming lose. Re-apply Dicor self leveling sealant to those areas.
2017 Salem Villa Estate 395RET- Ordered - Coming soon
2011 Coachmen Freedom Express 295RLDS- Sold
2015 F-250 FX4