Hi Marcin ,
Apologies for any inconvenience caused.
We always recommend using the latest version of our plugin. Old versions may include bugs, and we always include new features in our plugins. Also, if you keep updating WooCommerce, incompatibilities may arise between both plugins.
What we should try to investigate is what failed on your site after updating ATUM. You can check if anything is saved in the error log file when the plugin is updated and tell us where the problem is.
You can read here how to activate it.
Also, please note that we recommend updating plugins on a staging site before going production to prevent these issues.
However, if you decide to keep the old version installed, what you did (disabling the automatic updates) should work.
Best Regards,
José Andrés