Bundling in Magento is meh. Don’t use it. As Sairai has already mentioned, you need to use Advanced JS Bundling. Also check that you either use Advanced Bundling or Merge JS.
Quick setup guide for Advanced Bundling. Install nodeJS, npm and Reactjs. I personally use Magento DevTools installed as a Chrome extension. There’s a record button inside the extension. Use it to record how JS loads on Checkout. I suggest you also do it for other key pages in order to create a comprehensive bundle.js file that would include other performance-critical pages.
Ok so the next step is to create static content php bin/magento setup:static-content:deploy
You need to go to /pub/static/frontend/Magento/yourTHEME/yourLOCALE/ let’s say /pub/static/frontend/Magento/luma/en_US/ Also rename en_US to en_US_source
If you have put bundle.js to Magento root folder, then you need to execute it from there:
r.js -o build.js optimize=uglify2 baseUrl=”pub/static/frontend/Magento/luma/en_US_source/” dir=”pub/static/frontend/Magento/luma/en_US/”
There are more things you can do actually. We wrote this guide that includes a few good ones besides advanced bundling.