Hi,
As I said by email, I checked your CSV and I don't see why it would add the products to the main category. It doesn't on my end.
Note that if your categories are already created, you can simply delete the "parent_category" column from the CSV as the system will be able to link the product to the categories directly. Maybe that would help ?
I did a test on my end like below and I couldn't reproduce the issue:
product_code,parent_category,categories
my_prod_test_import,main category for test import,category of product for import