Background button is clicked automatically

Background button is clicked automatically

Hi

I've packaged my JQM App using phoneGap (android & ios). It works fine, but shows an issue like a background click/tap event is occurring is some cases.
ie If I clicked on a button in popup window the click is propagated to background button.
How can I prevent that?
Currently i've set an overlay behind the popup and set some delay for the overlay to remove(i dont think it's a good method), but bottom tab bar is showing same issue since overlay cannot be place here.