You can look at it both ways, he knew Aizen was sneaking around at that moment. Or he might of just felt his presense, Aizen letting him feel it.
But you can also look at it as Shinji not really caring about if that was or was not Aizen behind him. As long as he had some one behind him he didn't really need to use his maybe unknown power to tell if Aizen was there or not. It is just speculating but there is nothing else to do until next week's spoilers are out.
Plus I just want a new bad guy to appear here soonish and it doesn't seem like it is going to happen anytime soon.
