I'll handle this query for you about a PayPal transaction.
The missing amount you stated above sounds like a bank charge. If you connected your PayPal account as a regular online bank account in QuickBooks Online (QBO), you'll have to record the bank charge by hand.
On the Match transactions page, after you tick the appropriate transaction to match the downloaded bank transaction, you can use the Resolve Difference feature. Toggle its switch and enter the bank charge amount. Assign an expense account from the Category drop-down menu to track this amount. Fill in the other boxes as necessary, then click Save when done.
Take a look at this screenshot for your reference:
I suggest you take a look at this article: Use the Connect to PayPal app. It's an app you can sync to your QBO company that allows you to automatically record PayPal transactions. It includes bank charges, which will stop the situation you have to happen in the future.
Do you have other queries about QBO? Place them in the comments below, and I'll take care of it.