I've had this as well. The enemy demigod will be running from my Unclean Beast, with my claws slowing him he shouldn't be getting away, and yet my demigod will just sorta twitch and not chase after. I'll start spam clicking on them, and he'll continue to slighlty twitch and not give chase. Same thing with trying to run away sometimes. I'll give a move order to a point on the map well far away, and sometimes before they've moved 1/4 of the way there they'll turn and fight the enemy demigod giving chase.
I understand the need for some automation so my demigod can easily farm the NPC units without micromanagement, but when it comes to move orders it would be great is they 'always worked'.