"And [your defect]," he replied with a smile, "is willfully to misunderstand them." (Chapter 11)

"I have had the pleasure of your acquaintance long enough to know, that you find great enjoyment in occasionally professing opinions which in fact are not your own." (Chapter 31)

It could be argued that Darcy finds no natural defect in Elizabeth. If you consider how he came to admire fine brown eyes after a heated walk across country meadows (despite dirty skits); if you consider his deeply emotional conviction that Elizabeth cannot have always been confined to a provincial country life; if you consider how he hovered over her with admiration while she played the piano while both were at Rosings, then it is altogether possible to argue that Darcy was blind to any natural defect in Elizabeth. This might easily be confirmed by the way he fell in love with her again "in about half an hour after [he] had seen [her]" at Pemberley.

"You cannot have a right to such very strong local attachment. You cannot have been always at Longbourn." (Chapter 32)

The question is, then, why does he say that her defect is to "willfully misunderstand" people? That is explained by two things. The first is the smile with which he speaks the words. The smile combined with the words means that he is teasing her and suggesting that she is intentionally twisting his words as a tease to him since she cannot laugh at his self-disclosed defect of "implacable resentment." The second is his comment to her when at Rosings while he and Colonel Fitzwilliam are listening to her piano playing. Darcy says that he knows full well that she relishes saying things that she does not mean:

"I have had the pleasure of your acquaintance long enough to know, that you find great enjoyment in occasionally professing opinions which in fact are not your own." (Chapter 31)

Thus it is can be asserted and proven that Darcy finds no natural defect in Elizabeth and that his proclamation of a defect of "willfully misunderstanding" is a tease and not something that Austen intends for us to take as a legitimate characterization of Elizabeth either in fact or in Darcy's perception.

In chapter IX of Volume I, (ch. 11) of Jane Austen's Pride and Prejudice Miss Bingley, Darcy, and Elizabeth engage in a conversation regarding behavior. 

Elizabeth takes this opportunity to proof herself right about her assumptions regarding Darcy. When Darcy says the words 

There is, I believe, in every disposition a tendency to some particular evil, a natural defect, which not even the best education can overcome

he refers to his own flaw which is that, once he loses his good opinion of someone, this feeling will never change. Elizabeth paraphrases Darcy's admission by re-stating that Darcy's flaw is therefore to hate everyone. 

Yet, Darcy also takes a dig at Elizabeth and tells her that her flaw, as opposed to his, is that hers is 

to willfully misunderstand [everybody].

Darcy basically tells Elizabeth that, in her intense desire to prove herself and her ideas right, she misses many details that may change her opinions. As a result, even though she is basically accusing Darcy of being a proud "hater", she is clearly demonstrating a penchant for prejudice.