I have two pre-sentient species inside my territory, but they do not show up in the species screen, rendering me unable to uplift them. I have previously successfully uplifted a species (which went on to become an absolute majority in my empire, if you count all the genetic variations as a single species). I did disallow Native Enlightenment at one point to appease a bunch of xenophobic spiritualists, but allowing it again still doesn't get pre-sentients to appear on the list, even after waiting 10 years.
I don't remember if pre-sentients are supposed to appear as pops on the planet's Surface screen, but the two planets with the Stone Age Primitives modifier in my empire have no pops on them, perhaps they've been wiped out somehow, but the game failed to remove the planet modifier?
Update: I just found a pre-sentient population on a planet without a Stone Age Primitives modifier, whom I was able to uplift; that makes me think these are two separate systems, however I can not build an observation outpost on planets with that modifier, which you can do with sentient pre-FTL species. What can you do with those primitives?