To clarify before starting, all I know about this case is the links provided in the OP and having skimmed through the posts in this thread.

The main question here seems to be whose at fault, what went wrong?

Seeing how this all started with a boy getting shot by police let's start there.
But I'll say right now I'm not paying any attention to the kids skin colour, or to how friends refer to him as a good boy. What should matter is the actions that happened at the scene, not how the kid was outside of the situation or what skin colour the kid had.

From what I gather the boy was surrendering after robbing a store, but ran at the officer?
If so... If you just run at an officer with a gun you're going to get shot, they have no way to know if you intend to be peaceful or not. May the kid have made poor judgement or not, you can't exactly blame the officer for shooting if he was being charged at. Though also being Canadian I'll voice a similliar concern/confusion that Brovo did, the Cop should of aimed for non-lethal shots. Now, panic happens, accidents happen. But this did not seem like a case where the officer could get away with purposely aiming for lethal shots.

But then there's the protests that sparked as a result. Now, I think the whole "Black racism" claim the protest is doing is just idiotic, the kid charged at an officer and got shot. That kid happened to be black, that doesn't make it a hate crime, that makes it a kid who just happens to be black made a poor decision. And before anyone argues this happens to black kids more often, that is true. But also note that the poor/bad neighborhood's tend to have more black people than other places do. So obviously if more black people are exposed to shitty environments, more of them will resort to crime, resulting in more cases with police. This is not a racist officer issue, but rather an issue of how children are led to crime by poor environment and upbringing.

The protests themselves? A protest needs a cause, a point, one that will improve things. Simply trying to piss off the cops is not a legit protest... and if you're purposely stopping cops from doing their job, and yelling at them because you hate cops... That's not exactly a peaceful protest, that's causing a ruckus. And if while doing this other people are robbing stores and you are consciously stopping the cops from stopping the thief... you are now an accomplice to the theft. You are no longer doing a peaceful protest, you are committing a crime and are logically subject to the same punishment in accordance to law as the thief you were just covering for.

So I also really have no sympathy for those who took advantage of this incident to give police shit and/or to burn and rob shops. 
And since the investigation of the original shooting is still ongoing, that means no one has enough info to determine if the cop was at fault or not so I can't really make a final statement either. I can only say that if the boy really did charge at the cop, no one should be surprised that the trigger was pulled.