"I was really pissed off the academy left out my sister Alexis in the memoriam, because Alexis had a great body of work, but Alexis was one of very few trans artists that worked in the business," she told ABC News.
"At a time when we have trans kids that can't even go to the bathroom at school, you would think the academy would have a little bit more respect for a group of people that are murdered, and trans women of color are most likely to live in extreme poverty, making $800 a month, so I think the Oscars have a lot of learning to do."
The academy has not yet responded to ABC News' request for comment.
Alexis died in September at age 47. A member of the famous acting family, she was born Robert Arquette and began acting at age 12. She starred in a number of films, including "Of Mice and Men," "Bride of Chucky" and "The Wedding Singer," before documenting her gender transition in the 2007 film "Alexis Arquette: She's My Brother."
Patricia Arquette was not the only one upset by Sunday night's tribute, which honors people in the film industry who have died since the last Oscars. Australian producer Jan Chapman told Variety that her photo was mistakenly identified as that of Janet Patterson, an Australian costume designer and four-time Oscar nominee who died in October.
"I was devastated by the use of my image in place of my great friend and longtime collaborator Janet Patterson," she wrote in an email to the magazine.
Shortly after Bareilles’ performance, the academy posted a photo gallery of more than 200 recently deceased Hollywood professionals on Oscars.com.