I usually do this when I am interested in killing enemy troops in order to weaken their armies and avoid another fight after one or two turns (or in order to quickly crush the faction).
However, in some cases I simply quit since in those ones I would "hunt down" soldiers for nothing (and to me that's boring), for instance were I siege a city and the garrison would die anyway, or when I definitively destroyed a faction by killing the last generals and I don't have to seek renegade troops.
Today in my second Seleucid campaign I have just smashed the last three Bactrian generals in northern India with a 2vs2 huge battle, so when their two armies routed I simply left away running soldiers, either they would automatically disband or become vagrant rebels easily to defeat later with automatical resolution.
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