I've experienced this too. It's very reproducible with certain PDF files (like this one):
- Zoom in
- Scroll down so that the address bar is completely hidden (with only the domain name displayed in small text)
- Scroll up with a "flick" gesture (a faster swipe, release your finger while moving). I think you need to press down a little bit at the beginning, and move your finger downwards with an acceleration, as if you're trying to scroll faster.
As the OP showed in the video, it happens sometimes without a flick too.