Yeah, intentionally we did that for autocomplete element. Currently unlike to the CCK API, Form API do not provide separate autocomplete field for each value ( ie Number of values). For drupal7 autocomplete field is very much compatible to the tags, so we can put multiple tags with comma (,) separator but for CiviCRM comma (,) can be the part of contact name ( also we use comma for sort name too).
So to make this thing simple for CiviCRM, I just allowed single value for each autocomplete element by considering that user will add separate autocomplete field whenever he wants multiple contact references using autocomplete field.
Any suggestion regrading this?