This was driving me batty last night.
I fixed by:
Closing safari via double clicking the home button and swiping up.
Going to settings.
Open safari settings.
Clear clear history and website data.
Then go to advanced:
Open website data
Remove all website data.
When reopening safari make sure you open via a known link, else the previous pop up will repopulate website data and happen again. You will then need to redelete website data again.
This solved it for me.