Does anyone run into this problem as well? I’ve received a medal in-game for killing Warden Eternal and I’ve had at least 3 different times when it isn’t counted in the commendations. If this bug keeps going, I’ll never complete his commendation. 
Not quite the same, but I’ve had one instance where we killed Warden Eternal with 1 second left on the clock, got the take-down VO, but then were told we failed the mission.
I have a recording if people think I should post it.
You have to be doing heavy damage to get the commendation. I’ll to 6 get the medal, only 2 get the commendation.