If you get this error while installing a CU in any SharePoint Version, simply execute the installation on PowerShell window with PACKAGE.BYPASS.DETECTION.CHECK=1
If you have upgraded content dabases from different farms and have databases with missing featuers you can use FeatureAdmin. I have enhanced it a little bit 🙂
Click LIst All Faulty Features – Can take tike if farm is large.
Export the list for record
Either select one by one of click Delete all.
You should run this a few times to make sure your farm is clean.