what filter are you using to filter the values?
In most cases adding this to the top of your filter will work
global $post;
if (is_a($post, 'WP_Post') && in_array(get_post_type($post), array('acf-field', 'acf-field-group'))) {
// acf post types
// return whatever value is being filtered
return $original_value;
}