What version is your App Server and agent?
App Server 8.2.02
There were issues with the 8.2 and this error. Can you download this ZipKit and run against the targets that are giving you these errors: Blade ZipKit - Component Template with Remediation - Patch Readiness for Windows
Also, it would be advisable to move to at least 8.3 SP3 since there are many enhancements between these versions. Current GA is 8.5 SP1 Patch 1. 8.6 is coming next month as well.
I don't want to make it where upgrading will fix your problems but there have been many fixes in the newer releases for issues with patching.