Let me preface my explanation by first saying that Nur Ab Sal is obsessed with Bastila and thus thinks ANYTHING in the story that had her do or act any different than what he thinks she should have done, is "wrong".
But this "bug" that he refers to is how on the Leviathan, no matter what you do, Bastila always is captured by Malak and falls to the DS, and that no matter if you're "killing" Malak in your fight, the cutscene kicks in where Malak freezes you. So in reality, it's not a "bug", but Nur Ab Sal insists it is because he doesn't like the idea that the character he believes is the most powerful Jedi in the game gets caught regardless of what you (the PC) do.