It is really hard to tell identify a problem of the genitalia without inspection of the external genitals (vulva). Rubbing the clitoris area stimulates the surrounding glands (major vestibular glands, minor vestibular glands and paraurethral glands). The paraurethral glands (there are 2 of them) are located near the clitoris. If the excretory duct of one of the paraurethral glands is obstructed, the secretion can't be released during stimulation and painful swelling on one side of the vulva can occur. It doesn’t seem to be infection but it can get infected in time. You can visit your gynecologist for an examination.