The inefficiency of H&C's attack against Hermione's mind is not evidence of a "simple mistake" on his/her part, but rather exceptional cleverness. Note that this attack has replaced something that would be detected (Legilimency) with something that cannot be (Obliviation). I myself take this as further evidence that H&C is Quirrell.
Were there other mistakes you had in mind?
Using obliviation wasn't a bad move, but H&C used it poorly. More specifically, he used exactly the same disguise he was running around in when manipulating Zabini, when a great manipulator would certainly change their appearance to suit the situation. Not to mention the entirety of his conversation with Hermione strikes me as, well, clumsy. Professor Quirrell can convince most people of most things without multiple trials, and even if he modeled Hermione as putting on a show of goodness H&C's methods are not the ideal way to convince someone like ...
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
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: one, two, three, four, five, six, seven, eight, nine, ten.
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: