@webmaster, We will add fix for the deprecated issues in our plugin in our future updates.
Now regarding the issue with the categories, we are not facing any such issue mentioned by you on our end. The categories are getting assigned accordingly(https://prnt.sc/EKeWQ7wMLxEF).
It seems there might be some theme/plugin conflict on your end. Just to be sure deactivate all plugins except WooCommerce , MultiVendorX and MultiVendorX Pro on your end and switch to some default theme such as twenty twenty four or storefront and check again.
If still the issue persists please do create a staging site where the issue is replicated and share the staging site url, temporary admin nad FTP access of your site with us. Also while sharing the access don’t forget to mark your reply as private.
