I had a spy in a city of another players. While talking to him on the phone he looked in his millitary advisor screen and, low and behold, my spy was listed and he could see exactly where I was.

This was a Pitboss game, if that helps.

Hmmm, I wonder if that's how ehammer knew that my spy was on his continent. I will ask him as well. I know he doesn't have spies. I thought he was just guessing. Now i am not so sure. I will ask him but he will probably not want to tell me, or he will surely lie. I may check this with world builder.

Can do this in single-player also. Military Advisor screen will show you not only if you have enemy spies in your empire and where those spies are located, but who they belong to. I figured someone would have mentioned it by now, so I never brought it up. Has this issue been already addressed?

well that just is not right! WTF fireaxis.:(