Try clearing the data of those apps.
Does this happen in every app? If so, then it might be a sign of malware infection.
If clearing app data doesn't help, try installing some antivirus software and do a full system scan.
Also, try switching off Internet or mobile data and opening whatsapp. If problem continues, it indicates a malware or virus. If it stops, it might be either a malware or adware. Try this:
Clear cache from settings. Turn off mobile data. Switch off phone and switch it on again. Keeping mobile data off, and open the app, or whatsapp specifically, and then all other such apps.
If pop up continues even after this, then it's a malware or virus problem. If it stops, but starts once you turn on mobile data, it's probably an adware.
In any case, a good antivirus like QuickHeal will get you rid of both of these.
Disable the app called Setup Wizard.
Settings > Apps > All Apps > Select 'Show system apps' in the menu > Find Setup Wizard, tap it and disable it. Done.