Well, the Jalapeno and Red bell have had root rot. My Jalapeno died because I didn't know what was wrong with it until my Red bell started doing the same thing. The leaves get super soft and droopy, and the roots are brown and soft. I pulled all the brown roots off of the Red bell hopefully that was what I was supposed to do. There were only a few short white roots left, thicker than all the brown hair roots but still not enough to support itself at its current sized.
When transferring plants from soil, CLEAN the roots completely, especially on the peppers. Also, spread the roots apart don't just dig a hole in your grow medium and plop it in. If there are chunks of soil and/or the roots are just in a ball, they will not dry enough between water cycles; the plant will drown.