Hmm...is there an alternate-universe version of the Sanctuary? The Orion that, since Lucifer went down, was never converted into a refugee ship?
Anyway, General Battuta, I just remembered - shouldn't the player be invulnerable in nightmare missions (and flashback missions, though I think he's already invulnerable during the flashback of his mother's and wife's deaths)? I remember getting killed by one of the Lucifer's beams as it was firing at the Orestes. While this isn't strictly a bug I think that if you're in a mission that isn't actually happening, you should be spared the trouble of death. (I noticed this sort of nightmare-real-death issue in the Babylon Project's Raider Wars, but that's no longer in development, so I just sucked it up.)
And I'm pretty sure there was a discrepancy in Mina Taylor's name somewhere in the campaign, where her name was given by first initial, middle initial, last name, and the first initial wasn't M.
Edit: Whoops, I found the AoA walkthrough on the wiki. I thought it would be linked to directly from the main AoA page. Grr.