You can hit the tab key to cycle through all your units that can still act.
So before you hit pass, tab a couple of times to make sure nothing can act.
I'd argue against a popup box before passing, because there's quite often that I pass then unpass, because I have a card in my hand that I'm waiting to use if necessary if my opponent plays something. Most commonly it's Negate. So I'll pass, unpass, opponent acts, I pass then unpass, opponent acts, and so on. Having to click another box every time could get rather annoying.