Yes, but we saw the actual event in Humanism, part 1. We saw it right up until the moment Voldemort cast the Killing Curse. The "small, small note of confusion" refers to what Harry realized much later: "Dark Lords were not usually scared of infant children." The confusion was about the reason Voldemort was so intent on killing Harry in the first place.
The reference to souls is simply because that's what Dumbledore believes, not because of any plot. Yes, the Killing Curse behaved bizarrely, but we're supposed to think "Why did it behave bizarrely?", not "That must be a lie!", especially given that it sometimes behaved bizarrely in canon.
If "Eliezer has pretty much told us that something is wrong with the story" and we don't know what it is, that means he lied to us in Chapter 43.
We saw it right up until the moment Voldemort cast the Killing Curse
You're misremembering the chapter, that scene ends like this:
And the boy in the crib saw it, the eyes, those two crimson eyes, seeming to glow bright red, to blaze like miniature suns, filling Harry's whole vision as they locked to his own -
The new discussion thread (part 15) is here.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 82. The previous thread passed 1000 comments as of the time of this writing, and so has long passed 500. Comment in the 13th thread until you read chapter 82.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13.
As a reminder, it’s often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: