First, it is slightly impolite to immediately assume that someone made a mistake like this without even asking anything to confirm it, such as if any missile troops were even present where the general fell.
Second, about the issue itself: Routing soldiers occasionally hit chasing ones. It occurs both in SS and CoW and I would not be surprised if it happens in other mods too. Light cavalry is usually the most vulnerable due to their low protection but even bodyguards and their generals can die of it, obviously. I don't know about the lack of message, it's too long since I experienced something like that.
A big issue in CoW 1.4.4 (haven't tried the latest) is routing units staying and fighting

while "routing", rendering them impossible to target (!!!)

. Something similar may be occuring in SS, perhaps a bug related to vanilla issues, when the routers suddenly strike back. I regularly find that routing enemy infantry is more dangerous to my light steppe riders than when unbroken (and that is long after all arrows have been used up and fire at will turned off).