An annoying extension of this is opening a Google maps link on mobile. It always prompts to open Google Maps (the app) no matter what. If you click no, its bugs the fuck out and opens an App Store link. If you click yes, even if you have Google Maps installed, it bugs the fuck out and opens an app store link. In neither case will it properly show the location on a first attempt. It's been like this for years. I'd ask what they're thinking when they came up with this, but I remain unconvinced that any such activity happens inside any Google offices today.

I think this is an Apple bug.

I’ve seen it with non-Google apps too. I’m not sure what causes it, but I believe sometimes you can long tap the link and select the correct option.

I believe the behavior where you say no and it still tries to open the app is because the default behavior on Google Maps links is to open Google Maps.