The Supreme Court has decided that Etobicoke-Centre does not need a by-election. You can find the text of the judgement here.
It was a close count, a 4 to 3 decision, which means partisan opponents who want to yell “Fix!” can keep doing so. But there is this in the majority judgement:
We are dealing here with a challenge based on administrative errors. There is no allegation of any fraud, corruption or illegal practices. Nor is there any suggestion of wrongdoing by any candidate or political party. Given the complexity of administering a federal election, the tens of thousands of election workers involved, many of whom have no on-the-job experience, and the short time frame for hiring and training them, it is inevitable that administrative mistakes will be made. If elections can be easily annulled on the basis of administrative errors, public confidence in the finality and legitimacy of election results will be eroded. Only irregularities that affect the result of the election and thereby undermine the integrity of the electoral process are grounds for overturning an election.
… On these five occasions in his reasons for judgment, when making crucial findings of fact as to the validity of the votes, the application judge misstated the onus of proof. Instead of asking whether Mr. Wrzesnewskyj, the applicant, had satisfied his onus of establishing an irregularity, the application judge asked instead whether Mr. Opitz had established that there was no irregularity, thereby effectively shifting the burden of proof.
Because the application judge misstated the onus of proof a number of times in the course of his analysis, we cannot be confident that he applied the correct onus in arriving at his findings: R. v. Couture, 2007 SCC 28,  2 S.C.R. 517, at paras. 85-86. Overturning an election is a very serious matter. In order to uphold the findings of the application judge, we must be satisfied that he not only appreciated which of the parties bore the onus, but also that he applied the correct onus in arriving at his critical findings of fact. We cannot be so satisfied.
In a nutshell: the nature and level of irregularity for the votes that Borys Wrzesnewskyj wanted tossed out, wasn’t bad enough to justify the tossing.
Frankly, the best alternative for Mr. Wrzesnewskyj is this: wait until the next election, then ask the electorate of Etobicoke-Centre to judge whether Ted Opitz has done a good job as MP, and if he hasn’t, vote him back in. Worst that can happen (from his point of view) is that he loses. Again.