Please check this out, it can help you: http://stackoverflow.com/questions/24177920/magento-soap-api-add-bundle-product-to-cart
Thank you @theMageComp . I tried changing the store to be the default store and made sure the option id's and selection ids were the same as the ones from the catalog_product_bundle_selection table but I still have the same issue. Please select options for product. saopfault is thrown by the API. Anything I can do to troubleshoot this issue? How can I know which options are missing ?
Update: I was able to make this work when I changed the search visibility to everything and used soap api v1 instead. Upon further investigation and putting some debugging codes in soap api version 2 I was able to notice that bundle_option was empty in version 2 even though I am already passing them. It seems to me that either there is something missing in the documentation or there is a bug, Could someone confirm please?