If there are more items of the same product in the cart, the plugin by default applies the upload rule only once: therefore, you will be able to only upload the files will be the same for all the copies of the product.
If the option “Split Products” is enabled, in the cart you will find one line for each item of the same product. This allows users to upload different files for each item:
This splitting option works only if users edits the product quantity from the product page. Yet, if you change the quantity from the Cart page, the items will not be split.