1) Tranq headshots can cause death. At least they did in HR
2) Non-lethal takedown animation can cause death if the character clips through geometry during animation
3) Asleep characters can accidentally be killed by physics when dragged. If they're difficult to drag because a body part is stuck somehow, pulling them can cause so much force that they fling into environmental objects and die. Also be careful about throwing them of course
5) Asleep characters can be killed by nearby explosions (cameras, grenades, etc.) or environmental hazards (electricity, gas, falling environmental objects like boxes, etc.)
It's extremely imperative to double-check each character you neutralise to make sure they survived the takedown/tranq shot and any subsequent body manipulation. Try your best to drag characters to safe shelter. For example, remove a character from the middle of the street and put them inside a safe storage shed (with heavy objects removed from the shed), then shut the door.
Being a pacifist is such a pain. Glad they did it that way.