There haven't been inquiries yet, so we're left to draw our own conclusions based on the evidence we have. In some cases there isn't a ton of evidence of any kind to deal with. Based on what we do know though, and on the apparent chain of command confusion surrounding the G20 I'd like to put forward a somewhat educated guess as to what might have happened.
When the black bloc riot started downtown police did nothing at all about it. What we have heard was that the police were concerned that some of the black bloc may have had firearms and going after them would have increased the risk and that the police's top priority was protecting the fence surrounding the G20 conference itself.
On examination neither of these excuses make much sense. First if police were concerned that the black bloc had guns then they did exactly the wrong thing. If you believe you are dealing with armed people you don't allow them to run around downtown doing as they please. Second, with 20,000 security personnel the police should have had no trouble guarding the fence and going after the 100 or so black bloc protesters.
Going back to the chain of command questions I'm guessing that after the smoke had cleared (within a few hours) that someone was angry about the decision not to pursue the black bloc. The government, after all, had spent 1 billion on security and when a security issue arose there was no response.
So the word went out that the "black bloc was hiding inside the peaceful protests" - I don't doubt that this is what line officers were told. They were also likely told something like "getting these people is a priority, so err on the side of arresting too many - everyone with a backpack or a bag of any kind is a suspect, anyone with a bandana is a suspect, anyone from Quebec or anyone from outside Canada is a suspect, anyone wearing black is a suspect, and if in doubt arrest." They weren't, I don't think, told this because it was true but because a large number of arrests (an all time record for Canada in fact) would make it look like the billion dollar security effort was effective, by the time all of the outcomes of the arrests were known (by the time the trials were over) the public would have forgotten about it. In the public mind the police had gotten the 'terrorists.'
That, at least to me, seems to match the way things work in Canadian politics at the moment, at least since Harper took over. It would explain everything that happened, including why police were so overly aggressive and why no one at a political level wants to talk about it.
I may have to amend this as more information comes out but without a full, independent public inquiry we are forced to draw our own conclusions so it is time to start putting the pieces together ourselves.