I can help you fix those multiple transactions recorded in your QuickBooks Online (QBO).
To resolve these duplicate records, we can change the default bank that is linked to the Sync with Square app. I'd be glad to show you how below:
Sign in to your QuickBooks online company, then select My Apps.
Find Sync with Square, then Settings.
Select Edit next to Basic Settings.
Update the default Bank account where Square deposits your money.
Select Save changes.
For a more detailed information and insights about Square, you can check out this article (scroll down until you reached the Common Feedback): Sync with Square hub.
If the same thing happens, I'd suggest contacting QuickBooks Online Customer Care for a phone agent to take a better look at this. A specialist will look up your account and further check on what's causing the multiple records of transactions in a secured environment.
Feel free to leave a comment below if you have follow-up questions about downloaded transactions in QBO. I'd be glad to help.