In the movie the Matrix Neo was supposedly guilty of virtually every crime they have a law for yet Neo does not even know what EMP is. Trinity explains it to him. You would think he would have watched GoldenEye or at least played it on the n64.

Just thought that was interesting.

Not to mention this strange fog rolling in across the globe in certain areas. Not like the aliens ever used a global fog before to cover something up or spread a plague/disease.