I'd like to make sure we're on the same page. Do you see duplicate transactions in the Transactions page? If so, make sure to log in to your bank’s website and check your statements.
If you see the transaction twice, then your data was downloaded correctly. Otherwise, you may have your bank account connected twice.
You can go to the Gear > Bank Accounts. If the bank is connected twice, you can hide the extra account by clicking the On/Off icon.