A red flag showing on the black menu bar indicates there is a problem with the QuickBooks Online sync.

Click on the flag and then the error message to see more details. 

To see older sync history select View message history at the bottom of the message dropdown.

The message will give specific details about the problem, below is an example.

To resolve this, find customer in QuickBooks Online and update it to only have one email address. If this was the only error during the sync, the next sync should be successful.