It happens to me too. Game version is 1.3 Fallen Enchantress Legendary Heroes.
I found out that this bug tends to happen when player was using a maxed army (9 units including heroes) and the combat was took place in a small/restrained tactic battlefield (especially in attacking cities and combat in dungeon).
I feel the reason of this problem is that there are no enough default places to place your hero and other 8 units.
I also found out that it almost never happens in the early game when only leading an army with no more than 6 units.
It is so annoying that even if the player managed to win the battle with out hero, his champion will get one injury; or the player has to reload the game several times hoping the RNG will produce a different battlefield that can put their hero in.