The answer to this question can be found in Chapter 16, which is when Wickham discloses to Elizabeth his rather partial and completely untrue version of events about his past history with Darcy. After Elizabeth hears what Darcy accuses him of, she finds it troubling that he can have such a strong friendship with Bingley, when Bingley strikes her as such a pleasant and congenial individual. Note what she says after she hears what Wickham has to say about Darcy:
I am astonished at his intimacy with Mr. Bingley! How can Mr. Bingley, who seems good humour itself, and is, I really believe, truly amiable, be in friendship with such a man? How can they suit each other?
What puzzles Elizabeth therefore is the inconsistency that Mr. Bingley's relationship with Darcy suggests. If, as Elizabeth believes, Mr. Bingley is a good and generous individual, he would not have such an intimate friendship with somebody who, if Wickham is to be believed, is a completely unscrupulous and nefarious individual. However, Wickham manages to persuade Elizabeth that Darcy is so two-faced that he is able to charm and impress those that he wants to without revealing his darker side to them. Having believed what she has just been told about Darcy, clearly Elizabeth does not find this explanation unplausible, as her silence following it testifies.