Not sure if this is a MunkiAdmin issue, but I saw it with Munki Admin first.
So I removed all software from a manifest and deleted it. Upon saving, running Make Catalogs and reloading the Repo (That way the views are real time rather then showing the old catalogs), I started noticing references to the removed catalog on MunkIReportPHP. Does munki admin remove the deleted catalogs from the Manifests (which is what was shown but had not actually done) or is that a munki tools command that is run that is supposed to do that?