I've been having the same problem, too, except it's not on Safari, which is acting fine. I do not have Pokemon Go, nor have I ever installed it. I keep getting the pop-up on my Facebook app. It pops up whenever I click on a link within the app itself, so it uses its internal browser. The settings for the app in the phone's settings do not allow you to block cookies or clear browser history. I've done all the other steps mentioned in here, including clearing history/data from Safari and blocking cookies, even though Safari hasn't been the problem. I've also:
-Restarted my phone every time it pops up in Facebook
-Swiped the app up to close it, then restarted it
-Deleted and reinstalled the app from my phone
None of this seems to be working, and my facebook app is pretty much useless (<- that may not be a bad thing, I have sh** I should be doing instead). My phone is not jailbroken, either.