That happens when:
You're using the new Shopify checkout page editor.
Your theme has a checkout.liquid file
Follow these steps to resolve the issue:
(1) Delete your checkout.liquid file from your theme files (Themes > Edit code > search for checkout and delete it). It won't make a difference as when you're using the checkout page editor by Shopify, that file is not loaded.
(2) Add Honeycomb widget through the checkout page editor as an app. Go to Themes > Customize > Checkout > click Add app > Add Honeycomb. Then drag and drop it to show anywhere inside the page.