If those bubble things are hard, they're probably just root nodules, which often develop when there's enough humidity. If true, they're not dangerous at all and actually make rooting cuttings and transplanting more readily successful.
However, in the picture there where they're all grouped together on what appears to be a healed wound of your plant, it does look unusual. To test if they're root nodules, cut a plant off by the stem below the bubbles and stick it in a cup of water. If they're root nodules, the bubbles will turn into roots, and then you can plant your pepper again (but be sure to use a fresh seed-starting mix or you might get damping off disease, which will rot and kill your pepper). To decrease the risk of damping off and to increase your success rate, instead of cutting the stem you can pull up roots with the plant and keep them in the water, too.