I recently killed a dragon (near the loving stone) and I didn't absorb the soul. I have two theories on why this is: 1) I didn't deal the killing blow, so it's not mine to absorb or 2) there were other hostiles around so the absorb action didn't take place.
Any findings or other theories?
This issue should have been fixed as of Patch 1.2:
Fixed rare issue with dragons not properly giving souls after death
Regardless of who kills a dragon (player character or otherwise), the dragon soul will always be absorbed by the player character (spoiler: except when you currently have a particular set of Dragonborn DLC quests active). There a bug, though, regarding respawned dragons not giving up souls after death. This has been fixed by the Unofficial Skyrim Patch:
Fixed some encounter dragons not burning up nor giving the player a soul when slain (respawned dragons were not being properly reset)
most likely that's a bug, I experienced that the skeleton of a dragon I slew followed me through a quick travel
after some random digging around in the console (assuming you're on pc) then to bypass this bug type in the command to set amount of dragon souls your player has "player.setav dragonsouls x"
