Overview
If Quicken downloads transactions and matches them to your manual transactions (or you manually match the transactions from the Downloaded Transactions section) but they are matched incorrectly, you can Unmatch the transaction.
Quicken for Windows Instructions
Quicken for Windows only allows transactions to be matched and unmatched while they are being reviewed in the Downloaded Transactions section at the bottom of a register. If you have the Automatically add to banking registers option enabled, you will not be able to review and manually match transactions. (Edit > Preferences... > Downloaded transactions > Automatically add to banking registers)

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Transactions can only be Unmatched if they have the "Matched" status under the Status column in the Downloaded Transactions section, meaning Quicken recognized a similar manual transaction entered prior to downloading your newest transactions.
If the downloaded transaction should not be matched to any register transaction, click the Edit button, and then choose Make Transaction New. Quicken changes the transaction's status to New.
If the downloaded transaction is matched to the wrong register transaction with a similar balance, click the Edit button and then choose Unmatch. Once the status of the transaction is "New", you can click the Edit button and choose Match manually to match to the correct transaction.
Quicken for Mac Instructions
1. Right-click the matched transaction in the register (matched transactions will have a blue pencil symbol to the left of the transaction).

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2. Select Unmatch Transaction.

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The transactions will unmatch and become two separate transactions again–one with a blue dot (downloaded) and one with an orange pencil (manual). You can now match the correct transactions by dragging one over the other and dropping.