Users are experiencing significant issues with the ITR Excel utility, particularly with tax calculations involving the 87A rebate and education cess. The utility incorrectly calculates cess on tax before the rebate, leading to discrepancies in the filed return. Other problems include 'NA' values in the JSON output and issues with online filing. Suggestions include filing grievances, waiting for the Java utility, or using the online portal, though the latter also presents its own bugs. Users are advised to carefully review generated JSON files and consider revised returns if necessary.