That's always confused me. It makes sense, sure, but it's never mentioned anywhere else before or after Morrowind. I suppose one possibility is that Vaermina simply modified the bloodlines, similiar to what Clavicus Vile apparently did with the Cyrodiilic vampires. Who knows. :shrug:
Or that Molag Ball who as father of the Monsters merely shelters them and thus got associated with them in folklore. When they sleep, the Cyrodiilic Vampires have the same nightmares as those in Morrowind so it's something that specifically comes from Vearnima.
It depends a little on what you want to do with the lore, but in most cases you can ignore this. Most vampires also seem to see Molag Bal as their father, so there isn't any obvious conflict that they could notice. Though if you're interested in the specific facts, then the Vearnima story gets real relevance.