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.
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2006 3000RK
2009 Ram 2500
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