Bosses with bosses turned off
I've seen bosses spawn in missions that have destroyable portals (CoT portal rooms and Portal Corp mission in Black Scorpion's arc) but not in regular missions when bosses are turned off. Is one of the other settings (team size or level) maybe causing bosses to spawn?
Kyle Al'Mordu - Lvl 50 MA/SR Scrap
Fusion Force!
TRIUMPH

I've seen it happen, don't know if there's a connection to what kind of mission I'm playing. I don't know what difficulty settings you play on, but for me, switching from x8 to x6 does the trick for me to prevent it.
It's happening on +0/X8 at level 50.
Are these genuine bosses, or bosses that have been downscaled to LTs? If you're facing (for example) Devouring Earth at +0/x8/no bosses, you'll be facing Greater Devoured with LT class hitpoints and damage numbers, but with their full boss-class selection of powers.
Incidentally, it's not the bosses that are giving you problems against Devouring Earth. It's the Quartz emanators summoned by LTs: they give +100% to-hit to everything in range.
Are there special missions that give bosses even though they are turned off?
I started getting Malta bosses in a normal mission thread, but thought it might be part of that mission that force bosses no matter what your settings are, but then I got the same thing with Devouring Earth in a morality mission.
So far, other enemy groups are fine, but Earth were throwing 3+ bosses into every spawn and they were eating through my defenses like they weren't there.