I had a great fight with 2 dragons and only 1 soul absorbed.
I have killed 9 dragons today and I have failed to absorb 4 souls.

5 dragons were random encounters and 4 were at dragon lairs.
I have only had 1 experience where the Dragon didn't decompose, I guess I'm lucky. Out of 9 Dragons you only got 4 souls? You either have really bad luck, or the game is messed up because you play it so much.
If its a dragon from a word wall that the game has registered you killed, then you won't claim a soul from it if you go back to clear the wall again.
I know some of my lv 60+ characters couldn't get souls anymore from dragon kills. Most were respawns. I had a higher chance if the dragon was a blood dragon or higher. An ordinary dragon would produce nothing.
if you kill a dragon from far away you don't get it's soul. until you go near it.
Happens to me a lot too. Haven't found a way to get around it.
Maybe some dragons are just stupid and don't have enough accumulated wisdom in their souls for the Dragonborn to use.
Just means that you have to kill more of the scaly buggers
Nothing wrong with culling the dragon population
Then you get to kill em twice
I really think of an answer as to why it's happening though, sorry The only time I've encountered this was if I revisited a word wall with a dragon.
The amount of blasphemy... Tahrodiis Joore!
Alduin feasts upon the souls of they who harm his children! Repent!
I am sure I read somewhere that sometimes you don't absorb the soul if you open a chest/corpse/another dragon before it starts to burn. Maybe you opened up the inventory of the first dragon you killed before the other one started to burn?
Hate to break it to ya but.........
Alduin was and is a push over, you yourself put up more of a fight when I faced you
I had a Legendary dragon that dropped and failed to burn last night. I felt a bit robbed because that was the first Legendary dragon I had killed at a lair, all the others had been random encounters usually in a town where I was too busy trying to kill the thing quickly. But I did remember the legendary battle i had knocking off the dragon that had been there previously, so it was not to bad. And at least I finally got a chance for a closer look at a Legendary Dragon.
I killed what I thought was a respawn earlier today...no burn up so I kept walking...outside of Riverwood I was jumped by a wolf...killed it and got a dragonsoul...WAH???
Probably just some kind of time delay, but still...
Naw, the wolf and dragon just switched bodies for the day.
I've only had it happen, that I recall anyway, whenever I've gone back to one of the Shout location where I've already killed the dragon to get the Shout. After a little time they respawn. No soul the 2nd (or 3rd) time through. Not seen it on anything else.
This^ Happened to me before. If you some how aggro a dragon from a word wall before you discover the wall, you don't absorb the soul.