The VAT charge is applied in addition to Stripe's product and service fees. You will be provided with a monthly tax invoice for the VAT that is charged on your Stripe fees. You can find out more about tax invoices here.
For Stripe to charge sales tax accurately, please ensure that your business address is up to date. Head to Business settings in your dashboard to confirm that Stripe has the correct information.
Find out more by taking a look at the articles below:
Global Taxation of Stripe fees