Yes, you can exclude those since you've already recorded those transactions in QuickBooks Online (QBO).
Amounts or transactions that'll be posted to your QBO account will depend on the on what we fetch from your online account. You may check with Square customer support if they can stop adding those full amount.
I've got an article that you might find helpful: Sync with Square Hub.
Let me know if there's anything that I can help. I'm always here to assist. Have a wonderful day!