Are you using a Wysiwyg field for a shortcode alone? Or is the field being used for content and shortcodes?
If it’s shortcode only, you could try changing your Wysiwyg field to a standard text field, then use the following PHP to activate the shortcode this way:
<?
$shortcode = get_field('my_shortcode');
echo do_shortcode($shortcode);
?>
Untested, but should work.