Some minor grievances & problems I have encountered:
On Tatooine, when being approached by the alien that reveals that Helena is in the cantina, Bastilla asks the alien if it has seen her mother before the alien has even started talking. Seems rather strange considering she is now the one who initiates conversation. Also, the cut dialogue in that conversation seems to just be different takes of the original, Bastilla asks about her mother twice now, this disrupts the flow of the conversation, and does not add a new point of view or anything relevant.
On Dantooine, when the first group of Mandalorians is threatening the farmer, the Mandalorian will shoot at the iriaz and never become hostile to the player, making the Jon quest line impossible. The Iriaz should be removed from the Matale estate module, and IMO Dantooine as a whole could use a reduction in the population of Iriaz. The Hutt inside of the estate is rather silly and If I had to guess I'd say he was cut for the sake of atmosphere as he is very out of place there.
On Lehon, the Sith Beastmaster is keeping Desert Wraid. I don't know how he could keep 2 apex predators the size of speeder bikes content, especially in that tiny room! This also affects gameplay as well, the beasts are too large to maneuver around in there, and can't get around the Sith or each other to attack the player. Something like kath hound or tuk'ata would make more sense to be kept as pets.