The "Unmerged changes on repository ..." alert is an Icinga check that tests whether there are pending unmerged changes on a git repository.
As of today it is used for the operations/puppet repo on various Puppet masters and for the mediawiki_config repo on deployment servers.
If the alert is about the puppet repo, the fix is to SSH to the relevant puppet master and run puppet-merge to check what is pending.
puppet-merge should tell you whose change it is and whether there are multiple ones pending and show you a diff. You probably want to ping the author of the pending patch on IRC and ask them if they forgot and can merge. Or you find it trivial enough and are confident then you just merge it yourself.
If the alert is about the mediawiki_config repo you probably want to ping a Mediawiki deployer and ask what's up. You can also check the deployments calendar to see what happened last or ask jouncebot when the next deployment is happening.