Wow, margin! (between the comment section and the answer section)
The screenshot is taken from Ask Ubuntu and it's actually the same on all sites where I don't have 200 reputation.
Is advertisement planned for mobile web or is it something else?
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We're eventually planning on showing an ad in that space, but for now we're running the ad serving code with no running campaigns in order to gather forecasts of how much mobile traffic to expect.
This particular problem boils down to a typo: When creating a zone to serve ads in, one of the options you can specify is whether the ad area should "collapse" if no ad is served into the container. This is what was supposed to happen here, but I had the wrong container name specified for that particular flag.
Fix should be deployed now. Thanks for the heads up.