These added aliases did not directly affect the start or progression of the quest in any way that I can fathom, but as soon as I returned and removed them, the quest would work just fine again.
To be specific, these were 10 virtually identical references that were called at a late stage in the quest to move 10 characters from an area. I expected there could be something broken later in the quest because of this, but the entire thing from the start?
Not only that, but I removed all code relating to them, so they were simply nothing more than aliases without a purpose. The quest was still broken. Then removing the aliases returned the quest to normal, so it seemed to indeed be the fact that they existed was breaking the quest.
If that's the case, I might just make a body removal quest that snatches these NPC's away from under the main quest, without encumbering the quest with more aliases.
Has anyone ever seen this before??