I'm assuming your trying to farm souls from the Dragon Alters (dragon heads on maps).
Those always bug; Intentional by Beth or not.
It appears that you can only get 1 soul from each type of dragon from each alter. When you level up enough, you will see more and more of the highest level dragon, and you will not see many lower level dragons.
Basically; Go to alter... Ancient Dragon - Soul Ancient Dragon - Nothing Ancient Dragon - Nothing Blood Dragon - Soul Ancient Dragon - Nothing Revered Dragon (DG) - Soul Blood Dragon - Nothing etc.