QuickBooks only depends on transactions imported from Stripe. If you're referring to the expenses as fees deduction, we can manually record them within your QBO account.
QuickBooks handles these expenses/fees by recording an invoice and payment without the fees. When recording a payment, make sure to deposit it to Undeposited funds. You can take a look at the sample screenshot below.
Afterward, record the payment with the fees by utilizing the Bank deposit feature. Here's how:
Go to the +New button.
Select Bank deposit.
Tick the payment you want to deposit.
Under the Add funds to this deposit section, enter the amount of the bank service fee charged to you by the credit card company as a negative amount.
From the Account section, select the Expense account.
Double-check the details. Once done, click Save.
To keep your transactions accurate, you can check these articles: