Have you tried to do a force restart of the iPad? This can fix a lot of software glitches that are happening much like rebooting a computer when it has a small glitch. The iPad Mini 4 does have a home button so you can force restart it using this method:
Press and hold both the Home Button and the Sleep/Wake button until you see the Apple Logo. If you see a screen pop up with a slider “Slide to Power Off” just ignore this and continue to hold both buttons. Once you see the device power off, continue to hold until you see the Apple Logo. Once you see the Apple Logo you can release both buttons and allow the device to boot as normal. Once it has come back up it will be ready to go and you have successfully restarted it. Check things again and see if this has corrected your issue. If it is happening with just one app, then I would suggest force closing the App (double click the home button and slide the app off the screen) and avoid it for a little while and make sure that it isn’t still popping up this window.
If this corrects the issue and you haven’t run the app for a while, then I would try it again, if the window pops up again, then avoid using the app and get in touch with the app developer and let them know what issue you are seeing so they can use that to troubleshoot and correct the issue.