Elections Canada normally doesn't get involved in those kinds of disputes. Obviously, they can have repercussions, but the fact remains that those decisions are made by independent commissions. That's very different from the provincial system, I want to stress. The independent commissions have to take into account factors such as communities of interest and, as in the case you brought up, language communities.
In that specific case, the Federal Court found that the commission had not given sufficient consideration to that criterion and asked the commission to do the job over again. Since the commission had been dissolved by that point, another one had to be formed. I won't get into all the details.
Situations of that nature can occur, but they are rare, if not very rare. Our legal system ensures that those who feel their rights have been violated as a result of a decision have the ability to launch a court challenge.