I work in digital advertising for a mobile app. We are all trying to block these native alert pop-up messages. We hate them more than our users. Basically it's malware that is injected through an ad, usually not even by the original advertiser, which makes them very difficult to identify and block. Also, because they happen sporadically, it's difficult to replicate the behavior on our end to track them down.
The best thing you can do is to take a full screenshot that includes the ad on the mobile device and send a screenshot to the app developer. Provide your location (city, state, zip) the device and operating system, and time that you saw the ad. Also, we are more than happy to provide a download code for our paid app (with no ads) for free to any users that send us this info.
We all use some sort of ad scanning technology, but even those aren't able to identify and block them all.