The right of passage is one thing, the freedom of navigation. The Canadian government's position is that these are internal waters, and there are others who hold that they are international straits and they have the right to go through there at any time and at points of their choosing. That could provoke conflict.
Of course, the resource issue you've heard and know about. Then there's the sovereignty claim: Is it national territory or is it not? Wars have been fought over far less than this.