To me it seems Frank thinks Emma suspects something in Chapter 26 when they discuss Jane's new pianoforte. Emma sees him smile, but he turns the question back to Emma, who might not have been smiling at all. So he thinks Emma might have caught him in an unguarded moment.

Miss Woodhouse made the proper acquiescence; and finding that nothing more was to be entrapped from any communication of Mrs. Cole's, turned to Frank Churchill. "Why do you smile?" said she. "Nay, why do you?" "Me! I suppose I smile for pleasure at Col. Campbell's being so rich and so liberal. It is a handsome present."
The subsequent exchange is full of double meanings and involves Mr. Dixon as "red herring". Frank declares pianoforte is an offering of love. Is he quite sure here that he put Emma "off the scent"?
In Chapter 28 it is clear that Frank has told Jane what he thinks is a joke about Mr. Dixon, because there are some looks and blushes and smiles on Jane's part, so Emma reproaches Frank, and I think that since Emma is trying to protect Jane, Frank sees Emma as his ally.
(Emma:)"You speak too plain. She must understand you." "I hope she does. I would have her understand me. I am not in the least ashamed of my meaning." "But really, I am half ashamed, and wish I had never taken up the idea." "I am very glad you did, and that you communicated it to me. I have now a key to all her odd looks and ways. Leave shame to her. If she does wrong, she ought to feel it." "She is not entirely without it, I think."

Frank is giving Emma more credit for acuteness than she deserves. :-)