Shipping Rates Not Applying

You may find that if you try applying Custom Shipping Rates to your bundles that upon proceeding to checkout, only the General Shipping Rates apply to the bundle. 

Bundable only supports General Shipping Rates at this time.

The technical rationale behind this is every time you create a new bundle in the app, it creates a dummy bundle product in your Products section in your Shopify admin.

For every unique combination of products ordered in a bundle, a new variant of that dummy bundle product is generated. 

Due to Shopify platform limitations, newly created variants do not auto-assign to Custom Shipping Rates and remain in General Shipping rates when the customer goes to purchase a bundle combination that has never been purchased before.

There is a potential workaround:

If none of your other products rely on General Shipping Rates, transfer all of your products that aren't bundles to Customer Shipping Rates while adjusting your General Shipping Rates to favour what you want for your bundles. 

For example: if you need Free shipping for all bundles, but a flat $10 for all other products - create a new Custom Shipping rate for $10 flat shipping and assign all of your products MINUS bundles. Then make your General Shipping rate free, and assign it to your bundles.