By default, if there are more items of the same product in the cart, the plugin applies the upload rule only once; therefore, the uploaded files will be the same for all the product units.
If the option Split Products on cart is enabled in the General settings, in the cart, there will be a line for each item of the same product. This allows users to upload different files for each item:
The splitting option works only if users edit the product quantity from the product page. Yet, if they change it from the Cart page, the items will not be split.