I think they pointed out many real problems, not just with the individual details, but with the way HPMOR misrepresents scientific thinking as a whole.

So, I think su3su2u1's strongest point is that the "Slytherin! Just kidding, Ravenclaw!" applies just as well to the story as it does to Harry; you might think it's about the application of science to magic, Harry thinks it's about the application of science to magic, but it's really not; it's about rationality, and the methods of rationality. As one of Eliezer's recent Facebook updates puts it:

In retrospect, one of the literary problems I ran into with Harry Potter and the Methods of Rationality is that there was no clear signal until the final chapter of what the story was about.

And much of this is a meta-point, rather than explicit text: Harry, little professor that he is, isn't good enough at rationality to avoid shooting himself in the foot, because knowing the concepts isn't the same as living the methodology.

(I suspect that Eliezer agrees with a sanitized version of this criticism. To clarify, if I recall correctly, su3su2u1 identifies Yudkowsky as author as also being Slytherin, which seems to me to be its own discussion that could get prickly.)