We have seen quite a few citrus fruit samples at the Extension Office in which the fruit is brown on the outer rind, primarily on one side but sometimes all over. This damage is caused by citrus rust mites. These small arthropods chew on the surface of the rind causing the scarring/browning. Although you may notice the browning now, when you are harvesting the fruit, the damage probably dates back to summer and early fall when the mites were more active. The mites avoid the sunny side of the fruit, thus the tendency for the browning to be mostly on one side, unless the fruit was shaded on all sides by the foliage.
Since the rind damage is superficial, doing nothing is an option because the fruit’s eating quality is not significantly affected. Mites are most active in the hottest months of the year and therefore treatments at this time are not recommended. If you wish to prevent some of this damage next year, apply horticultural oil sprays in July, August and September. Make sure and get good coverage of all foliage and fruit surfaces for best results. Oil should be mixed at a 2% concentration in water and the spray tank should be shaken often to prevent separation of the oil and water mixture. Avoid applying oil to trees that are drought stressed or when temperatures are above 95 degrees F.