The app is showing hidden variants from a discount or quantity break app
Some apps create what they call hidden variants to add some functionality, like applying discounts or different prices in different cases. For example, there are quantity breaks apps that apply different prices depending on the number of items purchased.
However, although they say that the variants are hidden, there is no such thing as a 'hidden variant' in Shopify. All variants are first-class citizens in Shopify and our app cannot know if they should be hidden or not because that information is not in Shopify, it's only in the third-party app developers' servers.
In our opinion, using variants for discounts or quantity pricing is not a good implementation decision.
As we don't have the meta-information of those variants, we cannot hide them and they will be displayed in the variant selector in the app. The variants are displaying in the variant selector because they are regular Shopify variants.
The only workaround that we can provide to mitigate the issue is hiding the variant selector. That way the first variant will be always selected automatically. This can be done in the Visual preferences page, which can be accessed from the main Preferences page and clicking the Variants section afterwards:
Please note that with this option disabled your customers won't be able to select their desired variants.