I'll do my best. There are two parts to your question.
How are charities being used for illicit activities? I don't think that I necessarily see charities being used for illicit activities. I certainly haven't seen anything illegal, and certainly nothing criminal. As for whether some of the rules are being broken in terms of what charities are allowed to fund, perhaps they are.
How can I answer that? Some of the types of activities that raise questions for me are things like how I've seen environmental groups funded to renew the commitment of opposition parties to a ban on oil tanker traffic. Charities aren't allowed to do that sort of political activity. I'd also question, for example, cultivating indigenous opposition on building relationships with communities along a pipeline route. Does that constitute charitable activity? That's obviously something for the CRA to decide.
To the second part of your question on how funds come into Canada, there are the obvious acceptable and normal routes. Charities in Canada can receive funding from any donor anywhere around the world and are required to disclose that on their tax returns. Most do. I have seen some cases where, for instance, U.S. tax returns say that a Canadian charity was paid but in fact the Canadian charity hasn't reported it. I've contacted some of those organizations and they have in fact said that they filed their tax returns incorrectly and would refile with the CRA. That's one route, which is just the normal entrance of money.
The other thing that happens is that sometimes a donor will make a payment to a non-profit society, say, and that non-profit society then funds the Canadian charity, so by the time the foreign funds get to the charity they've been Canadianized, if you will, through the non-profit organization. There are millions of dollars coming in that way that don't show up as foreign.