I was adding and removing spies fine but something happened that has caused my spies not to be able to be seen or removed on the enemy planet where I assigned them. If I go to citizen summary there are two spies shown as being assigned to enemy planet. But when I go to the planet it doesn't show any spy icons over the improvements any more and so I can't see where they are or remove them. I suspect another different enemy going to war with me might have caused this but not sure.
In citizen summary I also have a dead spy but it doesn't say where he died, when he died or how he died. Not sure if he was on a planet I invaded or not. Some more info on his demise would be nice. I didn't see any notification of his death either but I may have missed it.
Edit: reloaded save game and dead spy was on same planet as the other two "missing" spies and not the planet I invaded so not sure how he died or why the others are missing.