I'm using iOS 9.2 and I once accidentally tapped “don't allow” or something similar when WhatsApp was opening a link for Citymapper. It used to launch the Citymapper app, but now it goes to the less useful web interface.
I've looked through all the settings but I can't find any record of this preference to reset the permission.
Metadata on page:
<meta property="al:ios:url" content="citymapper://directions?endcoord=51.56819%2C-0.086512®ion_id=uk-london" />
<meta property="al:ios:app_store_id" content="469463298" />
<meta property="al:ios:app_name" content="Citymapper" />
<meta property="al:android:package" content="com.citymapper.app.release" />
<meta property="al:android:app_name" content="Citymapper" />
<meta property="al:android:url" content="citymapper://directions?endcoord=51.56819%2C-0.086512®ion_id=uk-london" />
citymapper://
url from Whatsapp. I pressed Cancel on the popup asking for permission to open the Citymapper App and nothing happened. Then I pressed the link again and the same popup appeared. I would suggest updating to the latest iOS version and the latest version of both apps.