Ghost windows in Firefox

The weirdest thing just happened to me: Firefox was using an excessive amount of cpu. Ok, that doesn't seem too unusual; but as it was constantly over 80%, no matter what i had open, i started worrying about the extra heating for my thighs... After some unfruitful searches (plus a couple of reboots etc), i finally restarted in safe mode; and there they were, two extra windows with flash-heavy sites that i certainly never requested myself. Most probably pop-ups that came from the sites where i downloaded emulators for my vintage gaming binge recently, judging from the contents of the offenders... Crazy, i had never noticed them before. Could it be that they really stayed hidden all that time, quietly(!) eating up my cpu??