Okay, I have been extremely wrong with a lot of things about how the trolls were created. Apparently I skipped reading that huge chunk of text that describes the pre-scratch Alternia. Or maybe I misread it. But now I'm confused about the ectobiology of the trolls and their ancestors. I know Karkat created 24 wrigglers. 12 were the trolls we know and love, and the other 12 were assumed to be the ancestors. So I'm not sure where the heck the original trolls came from. Or when they came from. Because apparently it wasn't in their own session. It's all very confusing.
The original trolls were cloned from themselves, as were the ancestor trolls, all in their own session. I'm pretty sure.
My own personal theory of how the Ancestors weren't created in their own session is that when the wigglers were sent through Skaia's meteor defence portals to Alternia, something happened to copy (Some of*) them and send them twice, once to Beta Alternia, and once to Alpha Alternia.
So only 24 were created, but 48 (36*) actually arrived, 24 (our trolls and their ancestors) to Alpha Alternia, and 24 (12*) (The players in the Beta session of Sgrub (And their ancestors, who are our trolls*)) to Beta Alternia.
* The asterix'd numbers are if only the Beta player group was sent back from the Alpha session and their ancestors (who are our trolls) were ecto-spawned regularly. The non-asterix'd numbers are if both groups were sent back, and the Beta players never did any ectobiology.
(After reading that back to myself, I can't tell if it would make sense to anyone else or not. Bluh bluh explaining headcanon is hard.)