For example: "You're welcome" is not intended to convey the message that the hearer is welcome; it is a phatic response to being thanked, which in turn is a phatic whose function is to acknowledge the receipt of a benefit.
Similarly, the question "how are you?" is usually an automatic component of a social encounter. Although there are times when "how are you?" is asked in a sincere, concerned manner and does in fact anticipate a detailed response regarding the respondent's present state, this needs to be pragmatically inferred from context and intonation.