I had a drop in CTR a few weeks ago, and it turned out that Comcast was blocking my site because they had determined that a site on the same server as one of my sites was doing bad things. So they just blocked that server and all sites on it. Since I don't have Comcast, I could see my site and it looked fine. But a lot of people could not see my site (or ads). Of course, I could also see in Analytics that we'd dropped pageviews.