I had this after installing 1.4 with two Blood Dragons. Both dead but they did not go up in flames nor saw I a soul trap. The third, an ancient dragon, then did give me his soul.
Someone told me that sometimes a dragon soul will not get absorb and that it has been like this since the release of the game. I have never observed this before even though I have killed maybe 50 dragons by now. Hard to say if this is now a bug or just a coincidence. One cannot roll back and check...