I don't know if this has been posted yet but in ME2, during the geth heretic mission Joker say: "You know it's just our heat emissions that are hidden right? They can look out the window and see us coming"
And in ME3, the geth dreadnaught mission:
Joker says "The only way they'll detect us is if you start singing the russian national anthem."
and "Hey, take your time, Commander. We're fine until they, you know, look out a window."
Admittedly, the normandy crew didn't start to sing, and there were no windows for harbinger to look out of, but I find it hard to believe Harbinger didn't see the Normandy
So Harbinger saw the Normandy, so it must have decided not to fire on the Normandy. It couldn't have possibly known Shepard's intentions (it would take fanfic and that to make up a reason why). People say the Normandy was not a threat, but it that would be difficult for Harbinger to know, unless of course Harbinger is capable of very good multi-tasking. Which would mean that the reason the normandy wasn't shot couldn't be that Harbinger couldn't fire on multiple things/concentrate on multiple things.
Similarly, harbinger does shoot lasers at everything running up,. so it's not as if it's like the parts where Shepard climbs onto a canon, and can only shoot one thing at a time.
This leaves the IFF as the only possible reason I can see about why Harbinger wouldn't shoot the Normandy. However, I can't remember ever hearing that the IFF stops enemy ships attacking, only that it allows you through the omega relay. And infact, in ME2 the collector things still attack the Normandy, even with this IFF. So, does anyone have a link to where this IFF thing is said to protect people?