Think about(s)
1. The Prophecy - it is told that the path of "The One" is ending in the source room. but it does not clearly says the war is over... yes morpheus say so but maybe he got that wrong maybe the prophecy is that "The One" will get to that "source room"and thats it.
Note that the passt 5 chose to reload the matrix and Neo chose to save Trinity. so maybe it says that "The Sixth One" will end the war and the war is ended not when he gets to "the source room" but when he makes the choice in the source room all the others made the reload choice and he chose to save trinity and by that choice ended the war not right away but will end the war.
2. The Arcitect - it is said that machines built the matrix and that the arcitect built the matrix which means the arcitect is a machine. The question is - a machine which looks like a human? or maybe the real world is not real? to that add the reload of the matrix we all thought at first that he means reload the world were people are living without knowing BUT the rebuilt of zion is a reload too no?