all in all, i have played probably about 30 foundry missions. 10 fed, 20 kdf.
The #1 problem, and probably the only real technical glitch I have seen has been, the need to talk to someone that isn't there.
I go through some great series, get to the end of the last mission, and it says that I need to talk to someone.
The circle is over this room in the map. The person I need to talk to isn't there.
Why? Most likely, although I can't confirm it, that person is surrounded by agroable NPC's that I need to kill and the friendly fire gets them first.
I can't talk to them and they unspawn.
Out of the 30 missions, I can't complete half of them because of this. Fustrating.

Yes, apparently AoE damage kills critical mission NPC contacts. Unfortunately there's no way to prevent this other than to try to make sure the combat happens nowhere near important characters. There's no invulnerability flag we can toggle in the editor.

I get around this by putting NPCs away from combat. I'll also use the "off-screen" beam-in effect by having you kill all of the mobs and be at a certain spot before the NPC will appear. But since you aren't near it when it does, you have no idea how they got there because you can't see them..

I had this happen both on my mission that I've built and on at least one that I was reviewing. I didn't realize it involved a friendly fire problem. well at least now I know what the problem is hmmm how to fix it in my mission...

I put a big huge box made up of invisible walls around the NPC so that no enemies could even come near it, and still had people telling me it wasn't there. There's no way that it could be friendly fire in every single case.

I have been told this is it, but I'm still not convinced that there isn't some sort of bug causing them to despawn. It's happening far too often to too many people for it to be careless playing.

I suspect AoE damage isn't blocked by invisible walls.

I have had this problem hit me too, the ironic thing being that combat was not taking place anywhere near the contact. I worked around the issue by setting the NPC to become "visible" after the last of the enemies were killed and via a component complete trigger, which I also used to trigger the dialog. I've tried to avoid using "Talk to Contact" anytime there is a remote chance of a fight happening nearby.

Ideally they will make NPC contacts immune to damage to prevent this issue.

ok. so there is no invulnerable toggle for NPCs. Just wondering. It is fustrating