One of my glitches was at the beginning, when you're using the gun turret to kill the Sith. If a Sith gets on your ship, then when you're done and Atton goes to start up the ship, he freezes there, continually making the motions, and it doesn't go anywhere.
My brother killed that squid guy on Nar Shaada because he got the little girl released. But then later, the squid guy was alive again and he had to re-kill him (the trap in the private room in that poison cantina), and so he got the wookie. Neither of us got Mira yet o_o;
If you go to the jedi council without Kreia, the game freezes as it pans over the empty grass in their old room. If you take her, it continues fine.
I can't remember my other glitches, but I know there were like, two others.