For my legion's last two bases, I have launched the killing shot. It was also my first attack on each base (not sure if this may contribute). And I didn't get any badges for either kill.

Its a known issue and has been around for a while, that if its your first shot on a base or a shared NPC and its the killing shot too, then it doesn't register.

Don't expect it to get fixed, as it has been around for a long time and there have been lots of patches/updates since it was noticed.