I'm not sure what's going on, I just re-played that part and after commanding the marines to get in the VTOL he lets emmerson know that the LZ is secure and he is leaving... Emmerson then instructs psycho to stay on ground and move on and infiltrate the Harbor which is where my Green Dot on the map leads. Something Like this happened to me while playing the first Crysis...I was supposed to meet Prophet at a cave entrance and when I got there the entrance was blocked. Prophet just followed me around while I looked for another way in and I ended up having to reinstall The game... The cave then was opened. Weird.