Your oranges were probably damaged by a tiny mite which uses its piercing mouth parts to remove fluid from cells on the surface of the rind. This causes the skin to dry out and discolor. The pest is called the citrus rust mite when it damages oranges and the silver mite when it damages lemons. On oranges the surface of the fruit turns a rusty to brown or black color and on lemons it turns gray and has a "shark skin" appearance.
Fruit damaged during its early development may drop from the tree or stop growing and not mature properly. Damage to fruit late in its development is primarily cosmetic. Discolored fruit can be eaten when they mature, but they lose water faster than undamaged fruit and do not store as long.
Citrus rust mites are very small and may be carried from one tree to another by wind, birds, rats, or other rodents and by people. Rust mites are worm-like and can only be seen with 20X magnification, but the damage they cause is easily detected with the naked eye if you look for it. Check developing fruit at several locations on a tree once or twice a month. Young fruit should have a uniform green color with a waxy surface. Colonies of rust mites produce small areas of dull, discolored skin where they feed.
If rust mite damage is detected treat the tree with a miticide product labeled for use on citrus. Products containing sulfur like ‘Safer Garden Fungicide’ control mites and have some residual activity after application. Horticultural oil like 'Sun Spray' and insecticidal soap control mites on contact, but do not have any residual activity and may need to be reapplied periodically. Good coverage of all plant surfaces is required for best control. If the soil is dry, water before treatment and do not spray trees during hot or windy weather.
By V. Lazaneo, Urban Horticulture Advisor, Emeritus, UC Cooperative Extension,