For the story mission “Critical Blowback”, monsters that appear near the bombs are allowed to aggro and attack a player even if that player is in stealth (for upwards of 20 seconds no less). This occured if I was in stealth before the monsters appeared – couldn’t tell if it would still occur if I stealthed after the monsters appeared.
Either way, it makes the mission pretty difficult and dumb, especially when it seems sorta intuitive to use stealth in the Order of Whispers HQ.