So I was doing the quest when Delphine the paranoid schizophrenic forces you to "show her" or "prove to her" that you are Dragonborn by killing a dragon in front of her
and absorbing its soul.
So we make the journey to the place where Alduin is raising that dragon from the dead and after much effort on my part killing it..
I had done the first part of freeing the stones in Solstheim since Dragonborn sort of forces its way into the main quest of skyrim by having those cultists attack, then come back to finish the MQ in skyrim.
Miraak appears and ... Takes the soul.. Meanwhile Delphine the freak says "Wait, something is happening"
Miraak says "This one is Mine , Dragonborn." takes the soul and zaps out.
I know there are special scripts active during this quest to stop other dragons from attacking..
Did they forget about stopping Miraak?
-scratches head.-
-edit-
spelling