Strange... since the pennywort plants are new, they may have gotten a little traumatized in transit. Any brown, floppy roots are already not doing anything, and should trimmed off so that the rot doesn't spread to the stem. Avoid cutting off all roots that appear healthy.
To be honest, you could cut off all the roots with Pennywort and it would grow back fine, as they're accustomed to being trimmed/getting chewed.
Hope this helps.