The annomaly, Neo, can differentiate between the real and the fake. In the end the reason he has those powers is because he is still inside the Matrix. They say Zion has been destroyed 6 times and rebuilt. The reason it is rebuilt is because those who are 'freed' from the inner Matrix are still inside of the outter Matrix as a whole but think that they are now free. So the freed are then killed so that the annomaly, Neo, cannot discover the other Matrix. But because he chose the other door he was able to be released into the outter Matrix again and when he killed the sentinels with his power that should not exist outside of a Matrix world. Also, remember how agent smith transferred himself into that one guy on the ship? How could he have done that if the guy was living, the only reason he could do it is because that guy went back to the outter matrix. Has this already been discussed?