Hello kylie654,
Welcome to the Apple Support Communities. I understand you may be running into some issues scrolling.
Can you provide more detail about the issue and what you mean by a pop-up within Safari? When you try scrolling, does the entire iPad or Safari app stop responding, or are you able to otherwise use Safari outside of the pop-up you mentioned? If the entire iPad seems to not respond, this is a great starting point: If your iPhone, iPad, or iPod touch won't turn on or is frozen.
You also mentioned two apps; are you experiencing issues with scrolling in apps as well, or are these the specific websites you're having the issue with?
Does it help if you Restart your iPhone, iPad, or iPod touch?
You might also try to Clear the history and cookies from Safari on your iPhone, iPad, or iPod touch and then test the websites again.
I hope this helps get you started.
Take care.