it could be from where the umbilical cord fell off. that normally takes about a week, but if it came off a little early, it may bleed a little. does it still have the shriveled up stump or is it gone? if it's still there and this looks like something else, i'd call and make an appt with the vet to check it out. kittens don't have a lot of their own immunity to fight off infection, so may need to be seen before anything gets worse.
hernias are on the inside of the belly & will look like someone is poking a finger on the belly from the inside out. there would be no bleeding on the outside, so i doubt it is that.
EDIT: there is no such thing as too young to go to the vet. if it is old enough to have been born it is old enough for a doctor to look at it and professionally treat it. we've had kittens that were mere hours old brought in to us, so three days should be no problem, really. just bring the whole brood along in the same carrier if you think it will be more than an hour or so. mom will be fine with it and they'll travel fine together. surgery isn't something they'd generally do at this age, but the vet can at least give you an idea of what's going on and what the future holds for it.