Why were bundle items not added as line items to some orders?

Firstly, please confirm that you did not disable adding bundle items as separate line items to bundle orders in your app settings.
If the above app setting had not been disabled, then the reason may be that this particular order was marked as uneditable by Shopify.
This means Shopify will prevent both the app and even the merchant to edit the order (to add the bundle items as line items).
Learn how to handle this Shopify limitation by reading:
Handling uneditable orders