Okja, starring Tilda Swinton and Jake Gyllenhaal, has been controversial because producer Netflix has refused to screen it in French cinemas.
The audience booed the Netflix logo, which appeared before the film started, and it then became clear the film was playing in the wrong aspect ratio.
After the jeers, the movie was stopped and restarted without explanation.
Some film journalists in the screening uploaded videos of the heckling on social media.
"The second time around the audience booed the Netflix logo again. But there was also some cheering at the same time and a warm round of applause at the end."
She added: "On Thursday, at the Wonderstruck screening, there was also some booing when the Amazon logo came up."
The screen went blank before the film was restarted
Indiewire film critic David Ehrlich tweeted: "Okja starts, huge boos at Netflix logo. Then film plays in wrong aspect ratio and Grand Lumiere almost rioted. Movie stopped."
The Telegraph's Robbie Collin wrote: "Cannes making an A+ case for the primacy of the cinema experience this AM by projecting the first ten mins of Okja in the wrong aspect ratio."
Blogger Elena Lazic said: "That didn't start well. Screen not open properly, significantly cropped at top... the boos at the Netflix logo were immediately followed by boos at the terrible projection."
The film is a South Korean-American adventure movie about a young girl named Mija who tries to prevent a multi-national company from kidnapping her best friend, a massive super-pig named Okja.