Not sure if it's a bug, an oddity of using not the latest update, or whatever: Whenever one of my soldiers finishes a transformation procedure (ie: Bio-enhancement unlocked from the Red Dawn drugs), they don't seem to return to their last position/job before said activity. Or at least they don't with the gym: Whoever did finish being upgraded, is removed from the gym. Moreover, the game doesn't even tell you when one of said improved agents is fully recovered.
I suppose that's because recovering agents from transformations are considered to be "wounded". Wouldn't it be better if they were "transferred" to your base instead of counting as wounded? That way the game would warn you of when an agent is finished with the transformation and returns to duty.