How do I reconcile and/or record when the bank cleared a paycheck for the wrong amount (too little) and then issued a debit for the difference?

I appreciate you reaching out to the Community, @AnitaLanz.

The reason why you're unable to match the following transactions is that we're unable to match two or more bank transactions to a single entry created within QuickBooks Online (QBO). 

However, if you're referring to regular checks, we'll need to delete the existing entry created and add the two downloaded transactions from the Banking tab to automatically add them to the correct category.

To start, select the existing entry entered within your company file. Then, proceed to the following steps to Add the downloaded transactions from your Banking tab to the correct category. Here's how: 

1. Find a downloaded transaction with the Add option in the Action column.
2. Select the transaction and review the recommended Category. 
3. Change the vendor or customer as needed.
4. Review and add any other information that may be mandatory or missing.
5. Once done, select Add.

You can also refer to this article for more information: Categorize and match online bank transactions in QBO.

If you're using QuickBooks Online Payroll, I'd suggest contacting our Customer Payroll Support. This way, they can thoroughly track your account regarding this behavior.

Here's how: 

1. In your QBO account, go to Help (?).
2. Select Contact Us.
3. Enter your concern and select Let's talk.
4. Start a chat with a support expert.

Furthermore, I've added this article to help you automatically categorize transactions from your bank: Set up bank rules to categorize online banking transactions in QBO.

You're always welcome to reach us again if you require further assistance with matching transactions. The Community is here to help. Keep safe!