I think, as Ivonne said, Emma values Mr. Knightley’s opinions highly and further I think she is a little shocked at their difference of opinion and the fact that unbeknownst to her by sloughing off Mr. Martin from Harriet she was also disobliging Mr. Knightley. I am sure she had no idea her friend could have any interest in the matter and suddenly Mr. Knightly, an equal, is there disapproving her castling of farmers, vicars and parlor boarders. Until then I think Emma felt secure in her superiority and in her opinions being right about Harriet and who was right for who—neither Harriet, by temper nor Mr. Martin, by situation could disagree or confront her with what she is doing but Mr. Knightley does and can. Emma cared not a fig for Mr. Martin and enticed Harriet to reject him without a thought but IMO her habit of valuing Mr. Knightley’s opinion has to intrude on the surety of her opinions in the matter and ought to force her to question her actions and the reasons for them.

"You have made her too tall, Emma," said Mr. Knightley.

Emma knew that she had, but would not own it, and Mr. Elton warmly added… (Chapter 6)