I opened a bug report on this about four weeks ago. There are several instances where the ejection mechanic is not working properly: end of alliance or open borders; troops that were at war with a city before you took it; etc. I had a scout I totally forgot about [it was healing in a country with which I had an alliance]. After it healed, I was no longer allied and it neglected to show me this unit; so it just sat there for ages. Also, I've had instances where one of my units didn't get ejected, but if i tried to move it all the spaces around it had red circles indicating I couldn't.