When working on a security privilege, you may receive this BP deviations when manually adding objects in the Permissions\Tables node: "Non-system-managed Tables resource with incorrect managed by value ". You can get the same message if you are adding as well objects in the Server Methods or Forms.
The fix is simple. In the ManagedBy property of each object you've added enter Manual. You will have the BP deviation cleared.
Getting this message made me recall that there is a page with the full description of the best practices you may get: https://msdn.microsoft.com/en-us/library/bb530207.aspx
On that page you get the message description (be aware that the texts will have placeholders), for instance the message above would be "Non-system-managed %1 resource with incorrect managed by value %2" and also what is the fix, "Best practice security check that a non-system-managed resource has Managed By value set to Manual."