It's my pleasure to answer your first post in the Community. I've got some steps to help you correct Square transactions.
We can batch Undo the Square deposits that are added incorrectly in QuickBooks. Then, let's enter the transactions as Sales Receipt and deposit them to the Undeposited Funds account. This way, we can make a deposit and select the sales receipts and add a line item for the fees.
Follow these steps below:
Go to the Banking tab on the left menu.
Click the account you need to work on, then go Categorized section.
Put a checkmark in the box(es) for the transactions you'd like to undo, then click the Undo button.
Create a sales receipt
Click the +New menu, then choose Sales Receipt.
On the Deposit to field, select Undeposited Funds.
Enter the necessary information, then click Save.
Then, make a single deposit and add a line item for the fee. Here's how:
Go back to the +New menu, then choose Bank Deposit.
Select the sales receipts you created.
On the Add funds to this deposit section, add a line for the fee amount.