After creating a username and password for the 365 command (https://admin.365command.com/Account/LogOn) it will then ask to enter the username and password to connect to Office 365. If the username and password entered in the page below does not match the same username and password for Office 365 the following errors will appear as shown in the second screen shot.
Confirm that the Office 365 password works by logging into the following site. https://portal.office.com
If the credentials cannot access that portal with those credentials, then they will not work for 365 Command.
Another test is to use Windows Azure Active Directory Powershell module to test the credentials. That is what 365command calls on the backend.
If you load that powershell module and call connect-msolservice it will prompt you for credentials.