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Pip alludes to the tendency of people to magnify the injustices which have been perpetrated against them and, then, to take an almost perverse pride in their wallowing in sorrow. Or, in the vanity of remorse--grieving for someone or something long past the time which a person has died.
The vanity of unworthiness is an excess humility, one beyond normal control. For instance, a person belittles him or herself long after the accident or reasons are in the current mind. It is a perverse pride that one takes in this wallowing in an emotion, in wearing this remorse, or unworthiness, or penitence, or any of the others past the point of normal length that Pip calls a vanity.