I've been having this issue for a while too. Play on console, only started about a month ago and in the last week have been discovering dead dragons all over the place.
Walked out of Dragonsreach and there was a wing poking through the bridge, he was spasming in the water... guess he drowned waiting to pounce on me...
Or a stalker maybe the Dragon wants to get freaky with the dragonborn
Clearing the cache should clear the dragon as well, if you are on the Xbox 360 just clear the system cache to get rid of it. Not sure how you would do it on the PC/PS3.