I have been randomly having this issue using safari on my iPad for a while now. It doesn't happen frequently enough to be a problem for me but it does happen. I will be browsing satellite guys and all the sudden an ad will take over the screen. It is a tiny iPhone screen size ad in the middle of my screen with a black background that blocks out the rest of the site until I hit a small X in the top left corner of the ad. When this happens I usually just force safari closed and relaunch the browser and everything is fine again.
Edit: next time it happens I will make note of the ad and try to take a screen grab on the iPad before I close it.