Okay, I figured it out. The JS actions ACF offers were the solution. So if someone else stumbles across the same problem, please have a look at http://www.advancedcustomfields.com/resources/adding-custom-javascript-fields/
If you want to initialize a new select2 for example use following JS
acf.add_action('append', function( $el ){
//$el is the appended element, in this case a row
$el.find('select').select2();
}
Thanks for this great plugin.