"No," said Darcy, "I have made no such pretension. I have faults enough, but they are not, I hope, of understanding. My temper I dare not vouch for. It is, I believe, too little yielding -- certainly too little for the convenience of the world. I cannot forget the follies and vices of others so soon as I ought, nor their offences against myself. My feelings are not puffed about with every attempt to move them. My temper would perhaps be called resentful. My good opinion once lost is lost for ever."

(...)

"And your defect is a propensity to hate everybody."

"And yours," he replied, with a smile, "is wilfully to misunderstand them."

I don't think Darcy implies that Lizzy wilfully misunderstands people in general. I think he lets her know that in this case she is wrong - Lizzy exaggerated Darcy's talk about his faults into a "you hate everybody". Darcy lets her know that she is wrong. His reply is another way of saying "Indeed you are wrong, I do not hate everybody. I never said such a thing", but instead he continues the "fault-theme" and tells Lizzy that if his fault is a propensity to hate everybody, hers is to wilfully misunderstand them. But Darcy doesn't hate everybody, just like Lizzy doesn't wilfully misunderstand people in general...