I can't think of a workaround to this as it's all out of "our" hands. If you can put in a support case, I'd be interested in if this is a "bug" or just not properly documented as a gap in functionality.
I replicated the same behavior. While looking at the metadata in the report that wasn't flagged, I can see Salesforce appends a .CONVERT
to the field. I presume this throws it off from actually matching
<columns>
<aggregateTypes>Sum</aggregateTypes>
<field>Opportunity.Your_Custom_Field__c.CONVERT</field>
</columns
I assume the button is just using the MetadataComponentDependency as it's mentioned in this workaround concerning the button not working. You can see the same behavior in the query in Dev Console using the Tooling API and the custom field ID (which you can get from the URL when on the custom field page). The reports with a converted version of the field fail to show there as well.
Retrieve metadata and CTRL + F will still work in this scenario and is probably your best (and potentially only) option here. A very weak workaround going forward is to try to communicate to always include both the field and "converted" field in reports together. Doesn't help you in this case with existing reports, however.