Mouseflow records user events inside the browser document (also called the DOM) and uses this for playing back the visit.
However, IFRAME and pop-up windows use a separate DOM than the original web page. This means that you can record and playback interaction in IFRAMEs and pop-ups, not as a part of the visit on the underlying page, but as a separate page view.
To track IFRAMEs or pop-up windows, simply insert the tracking code inside of these elements, as well.
Note: If the content served from the IFRAME is on a separate domain than the main domain for your account, you'll also need to whitelist the third party domain under Settings > Domains.