Toughness is a supernatural power. How things work does not have to deal with physics at all. In this case, think of Balder being killed by mistletoe; his magical invulnerability simply did not exist against it. Ditto for some types of werewolves and silver.
As for what works, the catch makes poison ignore extra toughness, it does not make it deal more damage than normal or ignore the normal defense rolls against it and the poison has to be poison. Use common sense; being whacked with a chocolate is not poisonous. Eating a chocolate is not nearly poisonous enough to deal even 1 stress of damage (equal to a short knife). But the sting of a wasp (weapon 0, attack 3 vs endurance) would deal stress normally if she failed the defense and not be absorbed by her toughness/armor. So would the toxic fumes from a building on fire (environmental hazard 4 vs endurance) but the fire itself (another hazard 4 vs endurance) would have to deal with armor and extra stress boxes from her toughness.
Gas grenades, poisoned darts, strong contact poison on a blade, snake bites, magical water attacks that create poisons, the venomous claws of red vampires; all of these would ignore her toughness.