Something else I found which caught me out - I dropped a stun nade which obviously billowed smoke but this was early so I wasn't worried. I moved on and forgot about it. The game crashed so I thought back to that nade and reloaded from a point after I threw it. I checked out the area which was now under FOW as I had moved away and there was still some static smoke, presumably in the state my soldiers last saw it. Once one of my squad go there to take a look it disappeared and I could finish the mission.
This is just in case anyone else has the same scenario