Go to your Transfer Reports screen, set the date selector to the date of that deposit, then click on the deposit. You'll get a screen showing all the details of that deposit - all the totals for the sales that were in the deposit, along with all the deductions. The reason for the large deduction should show up there. If that doesn't solve the issue, you'll need to contact Square's Support team to dig deeper into your account.
Judy T Shumway
