The damage and stun from the second part of morg's ult did not occur despite being well within range (throughout the ult). I had this happen in a 1v1 with Teemo in my last game:
I used my full combo (missed q, no item actives) on teemo. My ult activated correctly however I walked into a bush and was out of teemo's LoS (I could still see him) when my ult detonated, however it dealt no damage and did not stun and he just walked away. Teemo was not taking damage from my w (or other spells or AAs) at the time the stun should've gone off although he could have been ignited (not sure). At the same time, I was taking damage from toxic shot and ignite.
I've tried to include as much detail as I can remember so hopefully there's something useful in there.