When this occurs it's usually because important metafield data on one or more app variants has been removed. This is assuming the app's code has been installed on the theme. The app uses this data to control it's variants, and when this happens the app no longer is able to properly recognize the variant, and is unable to modify, delete, hide or properly use the variant.
There's a few things that can cause this:
- The apps variant was manually modified in the product section of the Shopify admin.
- An import was initiated in Shopify while the app was applied to the product that was being imported and overwritten without the app being paused beforehand.
- The product and it's variants was duplicated from another product that had Product Bundles applied to it.
- In rare situations another app can affect a product in such a way that the apps metafield data is cleared.
It's strongly recommended not to do 1-3.
In the situation where the Product Bundle variants and/or their pricing is showing on the store front, and it's verified that the problem isn't being caused by the apps code not being installed on the theme, it can be fixed by the following method.
How to fix this
1. Turn off the app's group, wait until its finished turning off. Refreshing the page periodically and seeing if the "changes currently being updated" message is gone is a good indicator that it's finished.
2. Go into the product edit page within the product section in your Shopify store. Look for an app variant that is still present despite the offer being paused (pausing the app should have removed the variant but if the app lost connection with it it will still be there).
3. Select and delete these variants.
4.Turn the apps group back on to have the app recreate working variants.
If you have many variants that need to be deleted, it may be a good idea to export all of your products as a CSV file and mass delete the extra variants in excel, and then re-import the products.