Download from Bank [Edited]

Are you talking about, for example, checking account transactions downloading into the savings account … and vice versa?
Have you recently had to reactivate or reauthorize accounts at this bank?

If that is your problem, you need to

• deactivate all accounts with this bank, one at a time
• Stop and restart Quicken
• Use Tools / Add Account to reactivate all accounts. Follow the procedure to sign on to the bank. When you get to a Quicken dialog screen showing the list of accounts found at the bank, very carefully LINK each found account to the correct Quicken account register: Checking to Checking, Savings to Savings, etc.
  Be sure to LINK correctly or you'll be back in the same bad situation with transactions downloading into wrong accounts.