I don't think it's from overwatering. Could be fungus, in which case using the diluted hydrogen peroxide - a bit on the leaves and also water the soil with it - should help. If it's BLS (bacterial leaf spot), with a plant so small you're better off just starting from scratch. Note that if the parent plant the seed came from was infected, the seed was infected, too. That plant is too young to just remove the leaves, and you see it's on the cotyledons, too. (In case you don't already know, cotyledons are the seed-leaves, not true leaves.) There's a chance it would survive if you pulled those off, but a slim one.