It's unlikely that even the most experienced players could tell you exactly why this happens, but it's very easy to lose in auto-battle what you could easily save in a normal battle. I had a situation where a Crag Hack at level 15 with 1 Black Dragon and 20+ attack/defense died on a Gnome Stronghold at level 20. I then tried for a long time to lose that battle, but even if I waited all the time and didn't attack anyone, they just died from the counterattack, with a maximum stack dealing 15-20 damage and receiving 140-180 in return. So, auto-battle is a mysterious thing, IMHO.