Hmm, what species is this? It's not P.edulis. And I've never had experience with that particular problem. Looks fungal, particularly the lower spot, which seems to have a radial form of damaged tissue with a darker outline on the spreading zone.

Hi, your Edulis seedling has some sort of fungus. Be sure to keep the leaves from getting wet, keep it in a cool, dry atmosphere with the brightest light available. Don't over water. Spray with fungicide sparingly.

Thank you both. Fungus I can try to deal with. It's already standing in a dry spot. Hardly bright, but with winter here it's the best light I can give it.

Don't know what species it is though, as it's grown from a seed from a random passion fruit.

My update:
Passion fruit plant is growing again after being inactive for most of the winter. Since the brown spots were fungus, I did nothing to it, merely snipped of the damaged leaves as the plant grew, figuring plants tend to outgrow fungus. The plant no longer has brown spots.

A few of the new leaves are more typical with 3 point leaves.