Code to reproduce:

    private void InitializeChart()
    {
      tChart1.Aspect.View3D = false;
      Line line = new Line(tChart1.Chart);
      line.FillSampleValues(10);
      line.Marks.Visible = true;
      line.Marks.TailStyle = MarksTail.None;
      line.Marks.Angle = 90;

      tChart1.MouseMove += TChart1_MouseMove;
    }

    private void TChart1_MouseMove(object sender, MouseEventArgs e)
    {
      int clicked = tChart1[0].Marks.Clicked(e.Location);
      this.Text = clicked.ToString();
    }

note that Clicked returns valid index as if the Mark was not rotated.