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Papyrus/Papyrus Developer Guide/Oomph Version Management
As of late February 2016 in the Neon development cycle, the Papyrus Main plug-ins and features and the Developer Tools are configured for PDE API Tooling and Oomph Version Management validation. One of the value-added capabilities of Oomph is flagging plug-ins and features that aren't included in any other feature, and thus appear to be slipping through a crack in the release. This only works when the workspace has all of the plug-in and feature projects of Papyrus imported.
If your workspace only has a subset of the Papyrus projects imported, then you can tell Oomph that this check is not appropriate by configuring the "check mode" in the Preferences: