I agree, the scene with Harbinger just letting the Normandy pick up the wounded team mates on the ground and leave without being shot at is illogical. And all the reasons people try to make up can be shot down with logic. For example, someone said Harbinger was reloading. But that does not make sense because those streams of molten metal the Reapers fire do not need to be reloaded and can be fired without much delay between each shot. And considering it was firing so much, it could have easily shot down the Normandy without much fuss and returned to frying all the ground troops, and it would only need one gun aimed and can easily keep the other aimed at ground troops. I could go all day explaining but it would be better to not have the longest wall of text ever in a comment, so I would create a blog or something if I wanted to do so.
I used to be a huge fan of the Mass Effect series, but after a year after Mass Effect 3, I am not much of a fan anymore. I am not going to describe everything wrong with Mass Effect 3 here, would end up being a wall of text for sure.
I am now into the Naruto series. Though there are flaws, I think every series has at least one flaw if it is long running or has more than a dozen episodes, but there are very few of the flaws that come close to the illogic that is the Crucible, Catalyst, and the Normandy picking up the crew right in front of Harbinger scene. The one flaw that does come closest, and by closest it is far from the horribleness of what is in Mass Effect 3 but still the closest so far, is Sasuke Uchiha’s escape from Deidra’s final explosion.