Hi Kharlo,
We’ve released new version 1.2.1 today, which should solve the issue with new products not getting category prefix.
Now in plugin’s “General” settings (in “WooCommerce > Settings > SKU > General”) in “More Options” section, we’ve added “Delay SKU generation till product is published” checkbox. When it is enabled, SKU is not created until you publish the product, so you have time to set category, so prefix is generated correctly.
Best regards,
Tom