Instead of accepting the transaction, do a right click on the new transaction and select manual match. you should be able to then match it to the onw already in the register.
This happens to me once in a while. One that is easy to correct than I have seen is that the date of the transaction already in the register is dated past the one just down loaded.
Try making some changes to the one that it should match to. Quicken will do a match once it is "happy"..
On recurring transactions I do try to resolve so I don't have to do it again, One time sometimes I just manually match.
I started training my wife several months ago on how to us quicken just in case something happens to me. The manual match has been one of those things hard to remember.
I have been using Quicken since the very early DOS days so its not always easy to train when it just seems ingrained.
Good Luck.
For transfers like this I always recommend that you set up and use a scheduled transfer reminder.Enter this reminder a day or two before the due date so that you have a proper pair of mated transfer transactions in your register already. When you download transactions from the bank after due date, Quicken should be able to match the downloaded transaction to the existing transfer transaction and not cause a duplicate or other problems.
There isn't enough information provided in the transaction download for transfer transaction for Quicken to automatically do it correctly, all the time.