Haven't you seen movies before where the filmmaker deliberately leaves questions unanswered? Children of Men and Blindness are other sci-fi type movies where a major story detail is left unanswered, but the purpose of the movie isn't to explain that detail, it's to present a world that exists under those circumstances.

I feel that all three of these movies (D9 included) depicted these worlds with incredible realism, and just like the characters in the movies, we have no idea how these things happened; we just live here.

To play along though, there are so many different reasons why things could have happened as they did to the alien race. Maybe they were in some type of interstellar war that resulted in the ship being disabled and banished (with the intelligent members executed) to Earth... or they could be the riffraff of the alien race and banished to Earth as punishment. Who knows, but either way it's irrelevant to the struggle from the human perspective.