Have noticed a bit of trouble at the Telos Academy.
As a male exile, I don't see the handmaidens. (Can't choose to fight them.) After leaving with atris (I don't know if the choices I made fubar this), I step onto the Ebon Hawk. There's supposed to be a cut scene I'm guessing with the other 5 stating that Briana is gone. Yet it just hangs there with Atris, then goes back to the Academy screen with you right in front of the Ebon hawk.
Have also noticed a bit of trouble dealing with the Red Eclipse saga. After I finish with them, the part where I get the holo from Visquis hits. I thought "hey, I wanna go kill the Serocco before I head to the JekJekTar" I try to head back into the refugee sector, and the cutscene where the Red Eclipse lands and takes the Ebon Hawk Crew hostage starts again, though the bug was pretty hillarious, as it led to duping Kreia, the Handmaiden and Visas so the cockpit got incredibly full! However once the scene ends, you continue playing on as normal. You don't re-do the Red Eclipse fight.
I'm also not seeing the quest line update for encountering the HK-50's. I kill one group and I get the "you must encounter two more" part in my journal. I encounter another group and it says "journal updated" but says the same thing. I encounter a third group, and this time the dialogue is different, but still doesn't update. But I'm not too far into the game yet, so that might change.
So far I like what I see. Played through Dxun (as far as I'm aware) bug free, as well as Peragus and all of Telos (bar the Academy.)