Hi Sundhara,
When you say you have an external frame popup are you referring to an <iframe>? If so, the only way to track clicks within the iframe is to also deploy DTM on the page that loads within the iframe.
This is not a limitation specific to DTM but all tag managers. This is due to the way iframe work. Iframe by design are meant to completely separate everything within the iframe from everything outside the iframe.
Thanks,
Jantzen