It has become a common concern about how to maintain different versions of manifests used with the Desired Configuration Monitoring Solution (DCM Solution). The current version of the DCM Solution does not provide a way to store version numbers within the manifest or report on the version number (in the out of compliance or in compliance reports).
However, there is a workaround which you can probably employ to keep track of your manifests for source control / versioning reasons. After editing a manifest for changes, and saving the same, you can provide the version no as part of the file name itself. For example, instead of naming a manifest ServerRole.xml, name it ServerRole_1-0-1.xml. The next time you edit the manifest, increment the version number appropriately and call the manifest ServerRole_1-0-2.xml. That should help identify the version of a manifest for source control reasons and also will help you figure out which version of a manifest resulted in the out of compliance while viewing reports.
It might also be helpful to see if an earlier version of the manifest was out of compliance but the most recent version is in-compliance while viewing the DCM Reports. This is just a recommended way of tracking your manifest versions which might come in handy and quick to implement. Thanks!