It's my priority to get this bank transaction concern sorted out and help get you back on track.
QuickBooks Online is dependent on the transactions that were transferred by your financial institution. For now, we can try excluding those transactions that are showing as deposits and manually run an update
From the left menu, select Banking.
On the Banking page, select the For Review tab.
Select the check-boxes of the transactions to exclude.
From the Batch actions drop-down menu, choose Exclude Selected.
After that run the manual update to refresh your banking.