In FlexiCapture 12 "The partner returned a bad sign-in name or password error. For more information, see Federation Error-handling Scenarios." error might occur during the export stage when Multi-Factor Authentication (MFA) is turned on for the user who is being used to log in to the SharePoint library. Even if SharePoint libraries are visible and FlexiCapture shows the "Connected" state in "Export to SharePoint" settings - it might still throw the error during the export stage.
This is a known issue for SharePoint Online and it is actual for FlexiCapture Release 3 Update 3.
In order to workaround this issue, please, consider using a service user/account without MFA when connecting FlexiCapture 12 export profile with a SharePoint library.
We expect this issue to be fixed in future releases of FlexiCapture 12.