Two bugs I found are not so much bugs as coding issues..
Firstly, as said above, the permanent war between the rebels and the Empire still won't work... The Empire start off at war with Hutt Cartel, and that's the only war going on, I think.
Secondly, I don't know about the other factions because I've just been hanging around Hutt space, but the Hutts don't give a damn about pirates, jawas, Tuskens and the like. They don't attack them, and the pirates don't run away from them. It's just odd...
Apart from that, the mods immense fun still

Though my ickle laptop doesn't like it.. I get an atrocious FPS.