If any item wants to be deleted from Key Value pairs , Always the last one will be deleted :

So in App_Plugins -> KeyValueEditor -> "KeyValueEditorController.js" we should change the delete code as below:

$scope.deleteKeyValue = function (item) {
    var index = $scope.model.value.indexOf(item);
    $scope.model.value.splice(index, 1);
};

at the moment ,it is

$scope.deleteKeyValue = function (item) {
    $scope.model.value.pop(item); 
};