The app creates bundle variants to represent the bundle discounts that a user can receive if eligible. Part of the code install for the app will hide those bundle variants from showing up on the store front. It works by detecting if certain metafield data is on the variant and if so then the variant is hidden.
Other apps don't have that code programmed into them to hide or not use those bundle variants, and if the app pulls the shopify variant information and works with it in some manner (such as displaying the variants in another format), then there's a chance that the bundle variants will be pulled as well.
Because we don't have any control over what these apps do were not able to stop these apps from using those variants, and you would likely need to contact the other apps developer to see what can be done on their end.
Our code in the Shopify store front uses the following if statement to detect if the "shappify_bundle.is_bundle" metafield is equal to true, and if so the variant is hidden.
This or something similar would need to be used in the other apps programming to detect this metafield on the variant so its ignored