The UserGroup Entity has these two properties
    public class UserGroup : BaseEntity    { 
        //....
        public RelatedEntityList<UserGroup> AllChildren { get { return null; } }        public RelatedEntityList<UserGroup> AllParents { get { return null; } }

The Entity's config is to related them Many to Many

    class UserGroupConfiguration : EntityTypeConfiguration<UserGroup>    {        internal UserGroupConfiguration()        {            this.HasMany(i => i.AllChildren)            .WithMany(c => c.AllParents)            .Map(mc =>            {                mc.MapLeftKey("UserGroupId");                mc.MapRightKey("ParentUserGroupId");                mc.ToTable("UserGroupsHierarchy");            });        }    }

Such that it is Many to Many on itself.

Would you expect DF to automatically populate the "UserGroupsHierarchy" linker table 
in the same way as a linker table between two different tables does.
It isn't at present!

Thanks
John