They’re following the law.

Never stated otherwise.

They never saw the vote. They can’t count it,

I get what you're saying, but it's still disturbing that EC can cause a mistake of this nature and not have the ability to rectify it.

Certainly this isn't the worst case of disenfranchisement by Elections Canada (see for example https://www.ctvnews.ca/politics/article/this-is-unacceptable-polling-station-problems-prompt-calls-for-investigation/ )

it has to go to court.

Thinking it over, there's a good counterargument here. Even if EC could directly order a by-election in this case (or even was given the power to just outright count the vote), someone would contest this and it'd likely end up before a judge at some point anyways. So might as well just go direct.