Leonard's mother is a therapist, thereby probably conversant with psychoanalysis, in which the technical term used by Freud is "the unconscious" as in mind. There are, however, three levels of mind in Freud: three levels
So, her sarcasm is based on her own professional jargon. And, when you have a lapse of the tongue or bungled act, this speech and action respectively are said to be due to the unconscious, the deepest level and not just under the surface (subconscious). Freud would not locate a lapse at the level of a subconscious. It would be said to emanate from the unconscious.
Slips of the tongue (lapsus linguae) are briefly explained here: lapses. These are also known as: Freudian slips, in English.
The Big Bang Theory contains surprisingly tricky jokes. This is one of them.