Ok new report, I think this one is legit, game upload is 1823.
Basic behavior is that I get to the point where I've run through all of my notifications and I hit end turn, and then I get a pop-up notification saying 'but there's a minor alien faction that wants to talk to you!?', which can be clicked on. I can do so and talk to the aliens; they so far have all been various rebel planets, Prime Ashdar and Orthin so far. Interesting enough, both of these rebel factions have the regular faction leader for their species. Also neither faction actually appears in the list of factions in the diplomacy list.
Edit: Also I 'encountered' at least one of these factions by systems being revealed via an alliance. Don't know if that makes any difference.
-Will
edited by sven: Should be fixed as of r18790. Thanks for the reports.