Windows patch analysis job reports a patch as installed but it is not found on the target. 

Or the patch analysis reports a patch as missing but the patch is not applicable on the target (both manual installation and remediation job) fails with 'Not applicable' error showing "(ReturnCode=-2145124329)"

When the windows patch analysis result seems inaccurate, the best approach would be to run DPDTrace on the problem target to get the detailed trace then open a case with BMC customer support with the trace log.

Make sure the following before proceeding with DPDTrace:
- the target OS is under full support
- patch catalog is updated successfully 
- those patches that are reported as missing are valid (not obsolete) - you can verify against vendor article or catalog (catalog.update.microsoft.com)
- If you observe old/obsolete/invalid patches present and not getting updated in the catalog even after successful update, then try creating a new patch catalog with the same filter and check if the issue persists

You can download and use DPDTrace GUI tool from the following link:
https://forums.ivanti.com/s/article/PatchTrace-Patch-Content-Troubleshooting-Tool?language=en_US



NOTE:
- select "9.3.2708" in 'OEM Version'
- you would need to manually place  & 'WindowsPatchData.zip' in 'DataFiles' folder as suggested in the above link (In case the target server does not have access to the internet)

The DPDTrace result (xml file or hfcli log) may show the patch status as below example:

[20180601151521-wsapp2253-TR.xml]
<Item Class="Patch" BulletinID="MS15-135" SQNumber="Q3109094" Superseded="false" PatchName="Windows8.1-2012-R2-KB3109094-x64.msu" Applicable="false" Status="Effectively Installed" Reason="Patch does not apply under the current configuration but may apply if some option is turned on."/>...