When Doctor Manette gets a look at Charles Darnay after the latter's trial, he reacts with an instinctive fear:

His face had become frozen, as it were, in a very curious look at Darnay: an intent look, deepening into a frown of dislike and distrust, not even unmixed with fear. With this strange expression on him, his thoughts had wandered away.

He appears to see a physical resemblance to the Marquis St. Evermonde in Charles' countenance, even though he is not yet aware the two men are related. However, the resemblance is enough to trigger an unpleasant reaction from the doctor.

However, it appears the doctor does have his suspicions. When he gives Charles his marriage blessing, Charles almost confesses his heritage. Doctor Manette interrupts him though, since he does not want to know the truth. He is afraid of the truth, which later hits him square in the face when Darnay is put on trial by the revolutionaries who wish to condemn him for his aristocratic blood.

At this point in the book, Dr. Manette does not know that Charles Darnay is a relative of the Marquis St. Evremonde.  He does seem to recognize him, and gives a look of distrust and concern, but his daughter Lucy is glad that Charles is released because she did not believe he was guilty of the crime with which he was charged.  Later, after Charles asks for Lucy's hand in marriage and Dr. Manette begins to suspect who Charles really is, Dr. Manette begins to fall back into the madness caused by his imprisonment.

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