Controversy arose over whether the Deputy Returning Officers of the Chomedey, Marguerite-Bourgeois and Laurier-Dorion ridings had improperly rejected ballots. In these ridings the "No" vote was dominant, and the proportion of rejected ballots was 12%, 5.5% and 3.6%. Thomas Mulcair, member of the Quebec National Assembly for Chomedey, told reporters that there was "an orchestrated attempt to steal the vote" in his riding. A study released months after the referendum by McGill University [Bc]oncluded that ridings with a greater amount of "No" votes had a higher percentage of rejected ballots[/B]. Directeur général des élections du Québec (DGEQ), Pierre F. Cote, launched an inquiry into the alleged irregularities, supervised by the Chief Justice of the Quebec Superior Court, Alan B. Gold. All ballots of the three ridings plus a sample of ballots from other ridings were examined. The inquiry concluded that some ballots had been rejected without valid reasons, but the incidents were isolated. The majority of the rejected ballots were "No" votes, in proportion to the majority of the valid votes in those districts.
Two Deputy Returning Officers were charged by the DGEQ with violating elections laws, but in 1996 were found not guilty (a decision upheld by the Quebec Court of Appeal), after it was found that the ballots were not rejected in a fraudulent or irregular manner, and that there was no proof of conspiracy. A Quebec Court judge acquitted a Deputy Returning Officer charged with illegally rejecting 53% of the ballots cast at his Chomedey polling district.
In 2000, the Quebec Superior Court denied an application by Alliance Quebec that attempted to force the DGEQ to give access to all 5 million ballots, ruling that the only authority that could do so expired in 1996. The referendum ballots were incinerated in 2008 after appeals were exhausted. In May 2005, former PQ cabinet minister Richard Le Hir said that the PQ coordinated the ballot rejections, which PQ officials denied.