Thanks for your suggestions, @alvarnell. On @treed's advise (DM), I tried disabling each of my extensions one by one and it turned out the culprit was "Adblock for Youtube™". It would throw that message when I visited seemingly random sites (eg. nytimes.com, forums.malwarebytes.com), and started happening only a few days ago. I've reported it on the "Adblock for Youtube™" support service: https://chrome.google.com/webstore/detail/adblock-for-youtube/cmedhionkhpnakcndndgjdbohmhepckk/support?hl=en-US
I just hope the extension was trying to generate benign advertising popups.. rather than anything more malicious like steal information.