The only way to have this diagnosed properly is to have your doctor check your genital area. It could've been a wart, old ingrown hair, or maybe a pimple? Pimples and rash can appear if you don't bathe right after working out. Warts usually don't just fall off after scratching them, and are commonly skin colored unless they become irritated... If you notice any more showing up, get checked out by a doctor while they are still visible...
Good Luck