When you say, you are tracking YouTube videos using a plug-in, which plug-in are you using? Also, is it safe to assume that the plug-in is an Adobe Analytics plugin?
In general, pop-ups are often contained within an <iframe> tag. These iframes are essentially their own browser within your browser, you typically can track something contained within the <iframe> tags. What we normally recommend, is adding your tracking code to the page being loaded within the <iframe> and have it report back to the same report suite.