This is an update to jQuery Mobile documentation for embedding 3rd party video player in popups which states

Note that the video will still be playing in the iframe when the popup is closed. If available you can use the 3rd party API to stop the video on the popupafterclose event. Another way is to create the iframe when the popup is opened and destroy it when the popup is closed, but this would drop support for browsers that have JavaScript disabled.You can avoid adding  popup markup in every jQM page and it adds only when needed.”

 

First sample below uses third party API to pause video on  popupafterclose event.
A demo can be seen here.

Second sample below inject an iframe to popup and remove it on popupafterclose event.
A demo can be seen here.