] What does JA mean by all this? Why should Darcy think it bad that Lizzy thinks always of the present?

I donīt think Mr Darcy meant something bad with his reply. I think he tries to find out more about Lizzy, and as she has done in their earlier conversations he tries to bait her by making an assumption about her that she might not agree with.

] And why is it implied that Lizzy did not mean to say what she did?

In my copy the sentence continues with ", for her thoughts had wandered far from the subject," I think that she is occupied in her mind trying to find a way to get back to their previous subject regarding Darcys treatment of Wickham, but she does not want to be too blunt about it. Her next subject is about mr Darcys character, a subject she thinks she has a clear view of from Wickhams story and Darcys own expressions. So her not knowing what she said might mean she did not listen to mr Darcy long enough to hear what he said and just answered something apropiate.