Bubbles can indicate water intrusion but not always. Have you inspected for any other signs of water and/or rot? I would be all over that roof inside and out just to be sure.
Otherwise, how large are the bubbles? I've been able to poke small holes or cut short slits and insert glue behind similar issues.
What you're likely to find is a thin plywood like Luan behind the vinyl covering. You can try peeling it all off of the plywood or replace the plywood. Just realize that there is likely styrofoam insulation glued to the backside of that plywood. It's not the easiest thing to deal with.
Be sure to eliminate any possible water issue before fixing the roof. Otherwise you will have a repeat performance.
