How to turn off the "Screen Overlay" setting?
Got insights from multiple answers here and other forums . 

Consolidating how I got rid of the issue : 


Go to Settings > Apps > (your app which is getting issue)
Press on Power button till window for Power off , reboot , airplane mode comes up
Hold on Power off option 
Select reboot in Safe mode 
Go to settings > apps > (your app which is getting issue) 
Select whichever permissions you want 
After Android M update , issues can come up in apps like Messenger , Whatsapp , Prisma etc. 


Let me know if any issues . 
Note : I am having One plus One mobile.