Just checked the removal of 3D markers with a tag, and it works correctly.
Problem in waypointMarker.instance.tag.
You set the tag for GameObject instead of the marker.
There should be:

waypointMarker.tags.Add("Waypoint");

I can't remove my markers 3D anymore. It use to work before (though i'm not sure when it breaks).

I add markers with :

 OnlineMapsMarker3D waypointMarker = OnlineMapsMarker3DManager.instance.Create(data.GpsCoordinates.Longitude, data.GpsCoordinates.Latitude, waypointPrefab);
        waypointMarker.instance.tag = "Waypoint";

And i'm trying to remove them with :

 OnlineMapsMarker3DManager.instance.RemoveByTag("Waypoint");

One thing i change recently is my waypoint prefab :  it's now a prefab with another nested prefab inside. Could this be the problem ?
Edit: i tryed with a very simple prefab and the problem is the same. Is the RemoveByTag function broken ? The tag is properly assigned when i check the marker instance in the scene view.