Auto Increment value for field collection
The Serial Field module should be able to do that:


  This module provides an auto-increment (serial) field.
  
  Unlike Drupal's built-in auto-increment node ID, which is global and
  shared by nodes belonging to all content types, serial fields are
  managed per content type (D6) / entity (D7). For example, the serial
  field of an Invoice instance will generate a unique sequential number
  (starting at 1, then 2, etc.) exclusively for Invoice instances.