Hi lili,
Apologies for any inconvenience caused.
I'd need more information to try to figure out what's happening.
Are you using only ATUM free? Or do you use any premium add-on?
Which version of ATUM plugins and WooCommerce are you using?
Did you try to execute the "Update products' calculated properties" in AUM settings -> Tools? Fixes that the issue as manually adjusting the inventory?
Best Regards,
José Andrés