This is a great question. As you can see from your other question, the Canadian Charter is a beautiful document that seeks to protect the rights of people. It wants people to enjoy life in the most abundant way. So, from a theoretical point, it is a near flawless document. However, I can see a few potential limitations.
First, when people exercise their freedoms, such as freedom of assembly or freedom to worship in whatever way they want, there can be conflict among the citizens. In other words, people have differences. There is nothing on this topic. And this is a very important issue.
Second, there is little mentioned about the natives who lived in Canada before Europeans. I would think that at least a sentence should be included about the natives.
Third, to write something is very different than enforcing it. This, I believe, is where most of the problems will be.
it is legal for the government to limit an individuals charter rights. limitations on rights have been used for quite a while, about the last 20 years. its used to prevent variety of objectionable conduct suck as cruel hate speech and obscenity.
hope this helps