I played one game where I had an agent placed on the planet. When I took the planet, my agent stayed in place and I couldn't remove him. He didn't show up in the espionage tab as either a placed agent or an enemy agent. But on the planet screen it still showed the Red Spy logo on the building I had placed there. I tried demolishing the building and rebuilding there to no affect, also tried quiting game and reloading.
I do believe this was the original beta though, and have not seen it since upgrading. Also, at the time I didn't have the crash program installed (smartexception I think it's called) and the game crashed like like 10 - 15 turns later. Started a new one after that so I don't have the save game anymore, sorry, wasn't thinking