Sort Entity Reference Fields
I recently faced a similar problem and I solved it using the hook_form_FORM_ID_alter hook so that I can have an overview of the changes before actually applying them. My idea was to set the weight of each entity reference field to the number that can be found in the referenced entity's title. In your case however, the "numbers" in your title are not actual numbers with decimal parts but 2 different numbers that happen to be connected with a period (the first number has higher priority in the ordering than the second).

In your case you should do something like this:

function YOUR_MODULE_NAME_form_YOUR_CONTENT_TYPE_node_form_alter(&amp;$form, &amp;$form_state, $form_id) {
  if($form['nid']['#value'] == "22312") {  // The node id instead of 22312
    $keys = array_keys($form['field_FROM_ENTITY_REFERENCE']['und']);
    foreach ($keys as $value) {
      if (is_numeric($value)) {
        $weight = preg_match_all("/\d+\.\d+/", $form['field_FROM_ENTITY_REFERENCE']['und'][$value]['target_id']['#default_value'], $matches);
        if (empty($matches[0])) {
          $weight = preg_match_all("/\d+/", $form['field_FROM_ENTITY_REFERENCE']['und'][$value]['target_id']['#default_value'], $matches);
        }
        if (!empty($matches[0])) {
          $tempweight = explode(".", $matches[0][0]);
          $lengthtopad = (isset($tempweight[1])) ? 5 - strlen($tempweight[1]) : 5;
          $tempweight[0] = str_pad($tempweight[0], $lengthtopad, "0");
          $finalweight = implode("", $tempweight);
          $form['field_FROM_ENTITY_REFERENCE']['und'][$value]['_weight']['#default_value'] = $finalweight;
        }
      }
    }
  }
}


This solution is based on the idea that if from the 2 different-priority numbers that you have, you create numbers with the same amount of digits by padding the number with the highest priority with zeros, your final numbers will be properly ordered.

I assumed that the first number is single digit and that the second number can only go up to 3 digits. You can however adjust this to support more digits in the "decimal" part of the number. 

Just to give you a couple of quick examples of how the numbers will look like after the transformation described above:

1 -> 10000
1.1 -> 10001
1.2 -> 10002
1.10 -> 10010
2.45 -> 20045
2.456 -> 20456  

Of course, you can apply the same method to change the weights implicitly by using node_load, altering the weights and then using node_save to apply the new weights. It would work just fine, but with the solution described above, you edit the node-in-question and you can inspect the referenced entities and their ordering before deciding whether to save the node or not.