First, we don't shame here, and there's not a thing wrong with being a virgin, at any age. You are far from the only one, even if it feels that way.
Have you had any sexual contact at all? Oral sex? Grinding or rubbing? I ask because if you've had none of those things, it narrows the cause down a lot.
It could have been a comedone - which is really just a type of clogged oil gland - https://dermnetnz.org/topics/comedonal-acne/
The black stone would have been debris, and nothing to worry about.
Are you still getting them? You should see your doctor for how to properly treat them. You may need an antibiotic. Stop messing with them, though - if it's clogged oil glands, the oil from your fingers is only making it worse, and you could cause scarring.