^{When we disable the rule based on hit count using the option "Disable Rules Based on Hits" in SD, on right-clicking the standard policy/unified policy, it disables only a few rules. But when we generate the report for the disabled rule for more than 90 days, it shows more rules.}

This is as per the SD design

The rules which are not hit for a single time, will not display the last hit date in the Hit Count Details page and therefore such rules will not be disabled.

The same is documented here.