Was it one of the ones you get directed to kill in the Radiant bounty quests? IE, "go kill the dragon at Ancient's Ascent / Mount Anthor / etc."? If so, while those dragons do respawn, you can only absorb a soul from them once. So if you went to Ancient's Ascent (for example), killed the dragon and absorbed its soul, then got a bounty quest later on to go back and kill the dragon again, you wouldn't be able to absorb that soul a second time.
Otherwise...I've heard of this happening as a glitch occasionally. Not much you can do about it AFAIK.
