when zoom disappears, if you lead the card to the side, and then go back, then some of the tags can be displayed ..
The code took from the example of Yandex, just added his points

ymaps.ready (init);
FUNCTION INIT () {
  var mymap = new ymaps.map ('MAP', {
      Center: [54.809,56.1],
      Zoom: 10.
    }, {
      SearchControlProvider: 'Yandex # Search'
    })
    ObjectManager = New Ymaps.ObjectManager ({
      // To labels start to clusterly, set the option.
      CLUSTERIZE: TRUE,
      // ObjectManager accepts the same options as the clusterizer.
      Gridsize: 32,
      ClusterDisableClickzoom: True.
    });
  // To set options for single objects and clusters,
  // turn to the daughter collections of ObjectManager.
  ObjectManager.Objects.options.set ('PRESET', 'Islands # GreenDoticon');
  objectmanager.clusters.options.set ('Preset', 'Islands # GreenClustericons');
  Mymap.geoBjects.add (ObjectManager);
    ObjectManager.add (Geojson);
}

https://jsfiddle.net/5b9qud4w/2/
Example with my dots

Answer 1

As it turned out, all points coincided the ID, so there were such problems .. I made different IDs and all starts to work correctly