I'd like to help you get to the bottom of your discrepancy. You're going to have to do a reconciliation in order to get your register to match up with your bank. To do that, you'll have to determine which transactions should be in which deposit entry and then add the missing transactions to the incomplete deposit entry.
Follow these steps to align your register to your bank:
1. Log in to your QuickBooks Payments account.
2. At the top menu bar, select Activity & Reports, then Deposits.
3. In the Dates field, enter the date range of transactions.
4. Under the Fee column, select the deposits to expand. This shows all transactions that make up the batch deposit.
The report that you generated in Payments will be your reference. Use the report to correct the deposit entries.
1. In another browser tab, log into your QuickBooks Online account.
2. From the left menu, select Accounting, then Chart of Accounts.
3. Find the appropriate Bank register, then select View Register or Account history.
4. Find the batch entries you need to correct.
-Find transactions on the same date range you searched in QuickBooks Payments.
-Deposit entries auto-generated by payments have a memo of System-record deposit for QuickBooks Payments.
-The deposit entries dates should line up with the FUNDED date in your QuickBooks Payments.
5. Select a Deposit entry, then Edit.
6. On the Bank Deposit screen, scroll down to QuickBooks Payments. This section lists all transactions processed through QuickBooks Payments.
7. Using the Deposit report in QuickBooks Payments, compare the Deposit entry with the processed batch deposit.
8. Check off all transactions that are part of the batch deposit.
9. Make sure that the Deposit entry's total amount matches what you have in QuickBooks Payments Deposit report.
10. Select Save.
This will align your register to your bank. If you need further reference check out this article. If you need assistance with anything else. You can reach out to me here.