I live in Taif in Saudi Arabai. It is rainy from May to September ( on and off ) .we have a garden of pomegranate . The problem every year that when the fruits get ribe some get black powder fungus infection , some get gray white paste inside , and some dark brown rotten inside , and some get broken skin . We use insecticide and fungicide . I think probably we are not using the right control and probably the timing of control is not right . Also please advice me on Butriys fungus control in pomegranate . Thanks .
Aspergillus, Alternaria, and Botrytis are possibilities for what might be attacking your pomegranates. Botrytis infection of the fruit might explain the fruits you see which are rotted inside. This article and the attached article contain information on pomegranate Botrytis disease:
For control of all these diseases, the best option is to contact someone at a local university that has an agriculture program who may be better able to help. The reason is that the chemicals and other control options available are different in each country.