I worked as a front-end developer for an adnetwork for two years, so I take a little responsibility for your experience. I tried my best, but there just wasn't that much interest in getting it right.
Here's why I think we're all having a hard time with advertising in mobile. Basically, adnetworks are still learning how to do it right, the same way designers and developers are still learning how to do mobile websites right. The layout issue you mention comes from a conjunction of various reasons:
* Marketing thinks mobile == iOS, which sets limited expectations and for example means developers have a hard time getting a variety of devices to test on
* Adnetworks are likely targeting mobile with the same front-end infrastructure they use for desktop. Most of them still target IE6 so they're trying the same ideas
* Old iOS versions and many other webkit browsers have big issues with fixed positioning. First they didn't support it. When they did, they still had issues rendering while scrolling and firing the correct events
* Ads in mobile require a complex layout but the standard in the industry is that the website doesn't have to do anything but insert a script tag in the page. If there was teamwork between websites and ads, they could use better layout tools like flexbox
* No adblock on mobile (yet?) :P
Hopefully it'll change.