This is definitely happening (and still happening – ACF V5.5.3, WP V4.7).
dkeeling – a workaround is to check if the value is numeric, and then run it through get_permalink() if it is.
Your code would look like this:
<?php
$button = get_field('header_button');
if($button): ?>
<a href="<?php echo ( is_numeric($button['link']) ? get_permalink($button['link']) : $button['link'] ); ?>"><?php echo $button['label']; ?></a>
<?php endif; ?>
