Was there anyone else fighting it with you? Or other animals like a bear or horse?
On 2 occasions ive had dragons attack the town I was in and it never landed, and being a 2H Axe user I didnt have arrows or magic to hit it with so while I waited the town guards shot it and killed it. I got no soul. Another time my horse and several animals attacked the dragon as it landed. When it died I got no soul and only the bear was alive and in that fight im pretty sure it died while i was about to attack again meaning the bear killed it.
So im guessing unless you get the final hit it wont count as you killing it. Maybe for you some stray guard or passerby shot it just before you hit it taking your kill