Phantom lines appear on either the zero latitude or longitude axis if a point's latitude or longitudes settings are zero. Since both are zero in this case it will appear on both. This only occurs if the line width for the polyline is <= 1.

PhantomLines.m

- (void)viewWillAppear:(BOOL)animated
{
    [super viewWillAppear:animated];
    CLLocationCoordinate2D points[2];
    points[0].latitude = 0;
    points[0].longitude = 0;
    points[1].latitude = -6;
    points[1].longitude = 5;

    MKPolyline* polyline = [MKPolyline polylineWithCoordinates:points count:2];
    [mapView addOverlay:polyline];
    [mapView setRegion:MKCoordinateRegionMake(CLLocationCoordinate2DMake(0, 0), MKCoordinateSpanMake(10, 10))];
}


- (MKOverlayView*)mapView:(MKMapView *)mapView viewForOverlay:(id <MKOverlay>)overlay
{
    MKPolylineView* polylineView = [[MKPolylineView alloc] initWithPolyline:overlay];
    polylineView.lineWidth = 1;
    polylineView.strokeColor = [UIColor redColor];
    return [polylineView autorelease];
}