use the acf/prepare_field filter and run shortcoded on the field instructions. https://www.advancedcustomfields.com/resources/acf-prepare_field/
add_filter('acf/prepare_field/name=example_field', 'my_acf_prepare_field');
function my_acf_prepare_field($field) {
$field['instructions'] = do_shortcode($field['instructions']);
return $field;
}