My units is a lot older than yours and has several small bubbles as you described on the regular roof as well as the slide roofs. I think the EDPM material has just pulled away from the substrate. Probably spot not glued or pulled away overtime from the glue. I just keep an eye on mine and have for several years. Some get bigger but none have created a problem such as a leak. I wouldn't be too concerned unless they rapidly get worse.
2009 Ram 2500