I just destroyed an aug that was in a piece of gear, a ring that I was wearing, by right clicking it and selecting the Destroy option. I then realized that I didn't want to destroy it so I checked the Recover items on a vendor and it's not listed. It's not a huge deal as it's just a purchased type 3 aug, so I can go buy it, but I figured it should show up in the Recover tab if destroyed so it can be reclaimed with a token of reclamation.
This is not considered a bug at this time, it was implemented this way on purpose so that players couldn't destroy an augment and recover it to avoid the cost of a distiller (i.e. the Perfected Augmentation Distiller).