I agree with Rustler, hlg2482.

Mistakenly applied payments can unbalance your accounts and cause discrepancies in your records. To correct this, you'll have to undo your previous reconciliation first. After that, head to the Sales menu to clear the check payment. I'll show you how:

1. Select Sales from the sidebar menu.
2. Go to the Invoices tab.
3. Find and click the appropriate invoice.
4. From the pop-up window, click the View payment link under the Paid section.
5. Click the Clear payment button.
6. Hit Save and Close, then choose Yes to confirm the changes.

Once done, you may now apply the correct invoice payment. Then, reconcile your account again so they always match your bank and credit card statements. 

Additionally, here are some articles that you can read to help resolve common reconciliation errors and issues in QuickBooks Online:
 

• Fix issues for accounts you've reconciled in the past
• Fix issues at the end of a reconciliation

You can always find me here if need more help in managing your books. Just tag me in your posts and I'll get back to you.