Will App be terminated or suspended when updating to incremental version from app store?

Hello team, for our app we are utilizing location services and ibeacon services along with background mode, we request users to choose Always Allow access and in our code we use startMonitoringSignificantLocationChanges and Geofencing. When it goes to background we stop fetching the location…but we see Apple Location notification popup is being shown on.. From the attached screen shot we understood that our application has requested Locations in background for these many times and its showing map locations as well. Our users are getting annoyed with these popups. I would like to understand . On what basis apple shows these notifications to user, how they fetch the information. Is that our application hits for location and apple grabs it or when we choose always access automatically system makes these calls and saves information. Can we prevent this popup from displaying to users via code / iPhone settings ? Please clarify.