sorry i missed to mentioned the below
the selected values are getting duplicated when we delete it.
1. Select the options,
2. save the selected options
3. Load the selected options and set the selected options using below statements
var operatorDropDown = $("#Operator").data("kendoMultiSelect");
4. The values are getting selected
5. Delete the selected options by clicking 'X' Button
now see the duplicate options where their index is out of initial load.