The website USFunVideos.com is unremarkable in most respects, displaying snapshots of outdoor scenes and cooking videos. But recently the site contained something else: several tiny websites, smaller than a needlepoint.

These tiny sites, each the size of a single pixel on a computer screen, carried little content. But each served up ads, videos too small to see with the naked eye.

And the array of big advertisers—such as J.P. Morgan Chase , Coca-Cola Co. 's Minute Maid orange juice and smartphone maker HTC Corp. —were charged every time someone clicked on USFunVideos.com, and the tiny sites played the ads that couldn't be seen.

The sleight of hand is the kind of problem that ad executives and security firms say is now widespread across the Internet. Lured by the promise of advertising they could be sure was being seen by the right people, marketers are now contending with a deep bag of tricks that includes Web-crawling robots, server-based "drone pools" and the pixel-size video sites that has them paying for dubious Internet traffic.

Wenda Harris Millard, president and COO of the ad consultancy Medialink, estimates that as much as 25% of online ad revenue is wasted on fraud and piracy. Similarly, a February report from audience-research firm comScore found that 36% of online ad impressions, or views, are generated by nonhumans.