I ran into this issue too.
I tried to get the values in PHP-variables, to try to solve it in PHP:
$nr_of_wp_updates = do_shortcode('[wordpress.updated.count]') ;
$nr_of_theme_updates = do_shortcode('[theme.updated.count]') ;
$nr_of_plugin_updates = do_shortcode('[plugin.updated.count]') ;
$nr_of_backups = do_shortcode('[backup.created.count]') ;
But instead of PHP-variables that I can work with, I get strings that do not react to PHP functions in a way I would expect. The values of the variables are correct. In this example, there are 32 backups and 21 plugin updates. Every other value, like the string length, is not correct, though:
Var_dump of nr_of_wp_updates:
Var_dump of nr_of_theme_updates :
Var_dump of nr_of_plugin_updates :
Var_dump of nr_of_backups :
I would expect the length of the contents of variable $nr_of_wp_updates to be 0, but it is 25. It seems to be the length of the token itself ([wordpress.updated.count]).