I had same experience with Tokio 2 mision,
the last alien just disappeard while we was crossing one bridge in north-west part of the map, next to map edge.
this is small bridge, like viaduct.
once, I had mission in africa which I couldn't load. When dropwhip lands, game crashes, every time, so I had to give up on it
What to do with UFOs in RC6 when I can't shut them down?
Are you planning alien autopsy? it was great thing in original UFOs,
very supporting for story line.