Email attachments are not automatically added to the bundle (this is by design, as images in the email footer such as social media logos etc. would be included).
If you add the email to the bundle and then right click on it, you will see two options to add attachments.
You can add all attachments from the e-mail by clicking 'Add all attachments'.
Alternatively you can add individual attachments from e-mails by clicking 'Add attachments ...', selecting the attachments you need (1), and then clicking 'OK' (2).
Once the attachments are added, by default they will appear below the email the relate to, however they can be dragged and re-positioned in the bundle elsewhere. You can also remove the original email entirely and just leave the attachments within the bundle.