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So far for all but 3 of the kill or capture enemy agent mission types I've been able to compete them in stealth. One of them I, the agent was too strong to to a takedown and I had to breach the room and kill them, without silent weapons and a civilian as witness.

I didn't know that taking out too many guards would cause the agents to come out looking for my agents until I did a mission a few days ago to take out an enemy cell with three agents in it. I had taken out a bunch of the guards and two of the agents when I got a message saying something about too many guards not reporting in and the agents were suspicious and will actively search for my agents, destroy documents and turn security systems back on. It worked out better though since the last agent was in a spot that looked to be impossible to take out without being seen by civilians, and this caused them to come down where I was able to silently take them down.

So, anyway, last night I was doing one of the missions to kill or capture an enemy agent operating in the area (the two-man missions). The agent was in a room with no windows with a civilian inside, and too tough for my agents to perform a silent takedown on. I had an idea to take out guards and see if I could draw out the agent and then take her down silently in a better location. After taking out several guards, I got the message about the agent becoming suspicious and she came out of the room. I set up in a room with overwatch in case she came in, or if she went in another room I could breach it and take her down.

I re-loaded the auto save from the turn before to grab a screen shot to show how I was set up. I didn't dispose of the body in that room because I didn't think anyone would be able to see it laying on the ground below the window. However, the agent did see it, took cover on that wall between the window and door near where she is standing and somehow threw a grenade into the room with my two agents. The door is one of those metal doors with a barred window.

There is no way that agent could have seen my agents in that room, and no realistic way for a grenade to be thrown in there. The only reason the enemy agent is visible to me is because I saw her before moving into that room and used a spotter to keep her visible.
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Post edited September 08, 2018 by Mean.Jim
Yeah, the thing with the sight system is that it's entirely binary, an object either blocks sight or does not and a tile is either visible or not, object height is not simulated and a corpse is as visible as any character. We did so, among others, to make things mechanically more clear but obviously this results in some dead bodies being seen even though they are visually fully obscured by a low object. I hope we will be able to make some improvements for this. Similarly, I think, the doors with the small windows offer lines of fire and as a consequence grenades can be thrown through them - we should most definitely make some adjustments to them.

I will try to find that spot and reproduce the situation to see what went wrong exactly. In such situations a saved game is obviously the most useful thing you guys can give us and makes our job of reproducing and fixing errors much easier. So feel free to do so whenever you have the option.
I wish I still had the save, but I don't. I don't have iron man mode turned on, but I'm still playing it as if it's on by not re-loading when I make a mistake. When I re-loaded that save to get the screen shot, I played it forward from there doing exactly what I previously did to try and repeat the outcome to get a screen shot, but she wouldn't walk past that window again, even after several tries.