Normally, when my frigate pets refuse to dock (which is rather frequently, sorry to say), I can work around this by using another carrier command and then telling them to dock again. I might have to do this a few times, but then it works. I just got the Advanced Drone for my Khopesh, and the drones won't dock. At all. Even when damaged, they just hover around the back of the ship and don't enter. Definitely buggy. Even when I had my scimitar and its variants (tier 4, I think?) they would dock. Not all the time, but they would definitely eventually get docked.
Perhaps its time to hard-port hanger pets. Just a suggestion. I don't think it would be too game-breaking, though I don't know the coding involved in such an adjustment. However, I think that would solve a great deal of the docking issues involved.
::edit:: They finally docked. So this incidence rate seems to be roughly 6 out of every 8 missions.