Field collection table print row number
The field table collection module is kind enough to provide a specific theme function for tables that it outputs.

As such, you can implement a preprocess hook for the theme_table__field_collection_table() function and add your row numbers in there:

function MYMODULE_preprocess_table__field_collection_table(&amp;$vars) {
  // Add a new (blank) header
  array_unshift($vars['header'], '&amp;nbsp;');

  // Add an incremental count to each row
  $count = 1;
  foreach ($vars['rows'] as $key =&gt; &amp;$row) {
    array_unshift($row['data'], $count++);
  }
}