Software Updates/Bulletins are missing from the Patch Compliance Reports.
When running the Patch Compliance by Bulletin report those Bulletins are missing, yet when going to the Patch Remediation Center / Manage Software Updates Page - right-click the Bulletin and 'View vulnerable computers', there are applicable machines listed.
Reports only list applicable Software Updates that have not been Superseded.
The 'View targeted computers' drill down on the Remediation Center / Manage Software Updates Page does not take the Superseded status into account, for they are merely showing the Software that would be applicable to the updates. However, the Patch Filter will not target those clients if the vendor has deemed the Software Update was Superseded.
Run the Superseded Report and view if the Bulletin/Update was Superseded.