Just to clarify a bit, from what I've heard on Volition watch, the intro has a lot of problems with it, in terms of continuity or an accurate portrayal of the Battle of Deneb. The problem is that the intro was made by Interplay, not Volition.
But here are just a few things wrong:
-the Hades is crashed on Deneb. The Hades is a unique ship, and that IS the Hades on the planet. But the problem is that in Silent Threat the Hades never goes anywhere near Deneb.
-the beams from the Lucifer come from the wrong part of the hull.
-the Shivan fighter which kills the Hercules fires missiles from its gun points, and guns from its missile points.
-I think there's a Typhon destroyer there that shouldn't be, or something like that.
Basically, what the people were saying is that the intro is cool to look at. But its not really an accurate portrayal of the battle of Deneb. The intro has a lot of flaws.