I realize that my question is a bit ambiguous, so let me clarify. I've been playing Skyrim for a while now, and I'm up to level sixteen. I just resumed the "Missing In Action Questline" and decided to find the Thalmor camp. I haven't explored the area and solitude much, except for finding a few places. I fast travelled to the Haafingar Stormcloak camp and decided to head up from there. It is important to note that by this point, I have completed the quest, "The Break of Dawn", so I've been to Meridia's statue and absorbed the "Elemental Fury" word of power from the wall. However, I did not kill the dragon in that area at that time. On arriving at the Haafingar camp, I noticed a dragon flying around and roaring. It didn't attack me, or appear as a red dot, but the Stormcloaks did prep their weapons and look to the sky. I moved on and decided to explore the area a bit more in the direction of the Thalmor prison. I found that the dragon turned up dead, it's body near Volskygge possibly killed by the bandits there. As I passed by it, I absorbed the dragon soul. I reloaded, and tried doing a few different things:
Travelling to Meridia's statue instead and trying to get the dragon there. This didn't work out well. The dragon flew off, so I waited. It didn't come back in about 10 hours. I moved on to attempt two.
I reloaded an old save, outside of the Whiterun stables, just before I fast travelled (I'd just finished the "In My Time of Need" quest and had to move away from Kematu and Saadia to fast travel). I fast travelled to the Stormcloak camp and attacked the dragon there. I couldn't land a hit on it, so I gave it up as a bad job and decided to go towards an unexplored town. I discovered Dragonsbridge. On the way back, I found the dead body of the dragon near an intersection in the road and absorbed its soul.
In between these, I reloaded many times, and explored around to find the dragon a lot. I had no different results.
I've used console commands to delete the Gildergreen so that the sapling that I planted didn't seem to sprout out of it. I also used console commands to examine Lydia's inventory and to disable/enable Birna of Birna's Oddments in Winterhold.
The dragon by Bonestrewn flats wouldn't give me a soul. I think I might have killed it already when near the Eldergleam sanctuary for the quest to restore the Gildergreen.
I have the Dawngaurd dlc, but it is inactive. I had the "Data Files" section of the launcher grayed out and edited Skyrimprefs.ini in "My Documents" to fix it. I am not currently loading the dlc file.
I was wondering if anyone else had experienced this behavior or if this is a new bug I discovered. I was also wondering if anyone had a fix for this problem. As of now, I'm waiting ten days for the location to respawn (24 hours, rinse, wash, repeat) for the dragon to respawn so I can actually kill the damn thing.
UPDATE: I waited ten days, but that location did not respawn. I have cleared Meridia's dungeon, so it may be that I have to wait 30 days of in game time. I don't know. The dragon hasn't reappeared, and I'm no closer to killing the monster.
So, in summation, my question is, can dragons be killed by NPCs and still give me a soul? I'm especially interested in whether anyone has seen the same problem as well and if there is a fix. So do let me know.