rectification and correction process for IR-ISO from india local point of view

Need to understand the rectification or correction process for IR-ISO transactions from India Local point of view. We have had cases of wrong IR-ISO transaction done like wrong tax category attached or no tax category attached. Is there any rectification process from India local point of view.  

Cannot perform reverse IR-ISO or miscellaneous receipt or issue transaction as it would become difficult to make such transactions explain to excise authorities. Also without physical movement of goods performing such transactions would not be legally tenable

Has anybody come across such situation and any workaround for the same?