I don't know whether this has been said before, but I accidently found something out just now whilst playing.
You can find out if a settlement has an agent in it, including enemy spies in your settlement without requiring a spy or assassin.
Select a settlement (either your's or the AI's) and click on it so the settlement scroll appears (typically the one that displays enemy buildings and units/your governor and building queue). Very important.
For AI settlements, right click on any unit you see. For your own settlements, select the unit tab and right click on one of your units stationed there. The Settlement scroll must still be up!
Click on the magnifying glass icon to bring up the 'Find this unit's position on the map'. If an agent is in the settlement, the settlement scroll changes to that of the enemy agent. As well as having their face, it will say whether they are an enemy, neutral or allied. This gives you an idea who might be sending the agents into the settlement. This is useful for finding out whether there really is a spy in a settlement and whether you'll need to send in an assassin to kill enemy agents before trying to attack another faction's family members and buildings etc. For example, I've found out Numidia has a undetected spy in one of my settlements and we're not at war.
It's not massively useful, I'll accept, nor does it say how many agents there are, and you need another unit or agent in the vacinity to spot these 'hidden' characters but if you don't have an assassin or spy nearby, you can still spot them in advance.
You might be able to use this on armies out in the open to see if they have spies with them too.
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