I think it is frog eye spot or shot-hole leaf spot disease of noni fruit caused by fungus, Guignardia morindae. The main symptoms are appearance of sub circular spots (may reach up to 2 cm diam.) which are yellowish or grey in color. Some time you can see the black fungal fruiting bodies on the spot. This sporulating area may turn transparent and fall off causing shot-hole appearance.

Management:
1. Avoid wetting of leaf surface.
2. Spraying safe fungicides like Bordeaux mixture or any copper formulations controls the disease.